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-rw-r--r--tests/unit/correlation/__init__.py0
-rw-r--r--tests/unit/correlation/correlation_test_data.json18
-rw-r--r--tests/unit/correlation/dataset.json64
-rw-r--r--tests/unit/correlation/expected_correlation_results.json1902
-rw-r--r--tests/unit/correlation/group_data_test.json214
-rw-r--r--tests/unit/correlation/my_results.json388
-rw-r--r--tests/unit/correlation/test_correlation_computations.py65
-rw-r--r--tests/unit/correlation/test_show_corr_results.py226
-rw-r--r--tests/unit/utility/__init__.py0
-rw-r--r--tests/unit/utility/test_chunks.py19
-rw-r--r--tests/unit/utility/test_corr_result_helpers.py35
-rw-r--r--tests/unit/utility/test_hmac.py51
12 files changed, 0 insertions, 2982 deletions
diff --git a/tests/unit/correlation/__init__.py b/tests/unit/correlation/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/tests/unit/correlation/__init__.py
+++ /dev/null
diff --git a/tests/unit/correlation/correlation_test_data.json b/tests/unit/correlation/correlation_test_data.json
deleted file mode 100644
index 87d24e3..0000000
--- a/tests/unit/correlation/correlation_test_data.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "primary_samples": "C57BL/6J,DBA/2J,B6D2F1,D2B6F1,BXD1,BXD2,BXD5,BXD6,BXD8,BXD9,BXD11,BXD12,BXD13,BXD14,BXD15,BXD16,BXD18,BXD19,BXD20,BXD21,BXD22,BXD23,BXD24,BXD24a,BXD25,BXD27,BXD28,BXD29,BXD30,BXD31,BXD32,BXD33,BXD34,BXD35,BXD36,BXD37,BXD38,BXD39,BXD40,BXD41,BXD42,BXD43,BXD44,BXD45,BXD48,BXD48a,BXD49,BXD50,BXD51,BXD52,BXD53,BXD54,BXD55,BXD56,BXD59,BXD60,BXD61,BXD62,BXD63,BXD64,BXD65,BXD65a,BXD65b,BXD66,BXD67,BXD68,BXD69,BXD70,BXD71,BXD72,BXD73,BXD73a,BXD73b,BXD74,BXD75,BXD76,BXD77,BXD78,BXD79,BXD81,BXD83,BXD84,BXD85,BXD86,BXD87,BXD88,BXD89,BXD90,BXD91,BXD93,BXD94,BXD95,BXD98,BXD99,BXD100,BXD101,BXD102,BXD104,BXD105,BXD106,BXD107,BXD108,BXD109,BXD110,BXD111,BXD112,BXD113,BXD114,BXD115,BXD116,BXD117,BXD119,BXD120,BXD121,BXD122,BXD123,BXD124,BXD125,BXD126,BXD127,BXD128,BXD128a,BXD130,BXD131,BXD132,BXD133,BXD134,BXD135,BXD136,BXD137,BXD138,BXD139,BXD141,BXD142,BXD144,BXD145,BXD146,BXD147,BXD148,BXD149,BXD150,BXD151,BXD152,BXD153,BXD154,BXD155,BXD156,BXD157,BXD160,BXD161,BXD162,BXD165,BXD168,BXD169,BXD170,BXD171,BXD172,BXD173,BXD174,BXD175,BXD176,BXD177,BXD178,BXD180,BXD181,BXD183,BXD184,BXD186,BXD187,BXD188,BXD189,BXD190,BXD191,BXD192,BXD193,BXD194,BXD195,BXD196,BXD197,BXD198,BXD199,BXD200,BXD201,BXD202,BXD203,BXD204,BXD205,BXD206,BXD207,BXD208,BXD209,BXD210,BXD211,BXD212,BXD213,BXD214,BXD215,BXD216,BXD217,BXD218,BXD219,BXD220",
- "trait_id": "1444666_at",
- "dataset": "HC_M2_0606_P",
- "sample_vals": "{\"C57BL/6J\":\"6.638\",\"DBA/2J\":\"6.266\",\"B6D2F1\":\"6.494\",\"D2B6F1\":\"6.565\",\"BXD1\":\"6.357\",\"BXD2\":\"6.456\",\"BXD5\":\"6.590\",\"BXD6\":\"6.568\",\"BXD8\":\"6.581\",\"BXD9\":\"6.322\",\"BXD11\":\"6.519\",\"BXD12\":\"6.543\",\"BXD13\":\"6.636\",\"BXD14\":\"x\",\"BXD15\":\"6.578\",\"BXD16\":\"6.636\",\"BXD18\":\"x\",\"BXD19\":\"6.562\",\"BXD20\":\"6.610\",\"BXD21\":\"6.668\",\"BXD22\":\"6.607\",\"BXD23\":\"6.513\",\"BXD24\":\"6.601\",\"BXD24a\":\"x\",\"BXD25\":\"x\",\"BXD27\":\"6.573\",\"BXD28\":\"6.639\",\"BXD29\":\"6.656\",\"BXD30\":\"x\",\"BXD31\":\"6.549\",\"BXD32\":\"6.502\",\"BXD33\":\"6.584\",\"BXD34\":\"6.261\",\"BXD35\":\"x\",\"BXD36\":\"x\",\"BXD37\":\"x\",\"BXD38\":\"6.646\",\"BXD39\":\"6.584\",\"BXD40\":\"6.790\",\"BXD41\":\"x\",\"BXD42\":\"6.536\",\"BXD43\":\"6.476\",\"BXD44\":\"6.545\",\"BXD45\":\"6.742\",\"BXD48\":\"6.393\",\"BXD48a\":\"6.618\",\"BXD49\":\"x\",\"BXD50\":\"6.496\",\"BXD51\":\"6.494\",\"BXD52\":\"x\",\"BXD53\":\"x\",\"BXD54\":\"x\",\"BXD55\":\"6.263\",\"BXD56\":\"x\",\"BXD59\":\"x\",\"BXD60\":\"6.541\",\"BXD61\":\"6.662\",\"BXD62\":\"6.628\",\"BXD63\":\"6.556\",\"BXD64\":\"6.572\",\"BXD65\":\"6.530\",\"BXD65a\":\"6.280\",\"BXD65b\":\"6.490\",\"BXD66\":\"6.608\",\"BXD67\":\"6.534\",\"BXD68\":\"6.352\",\"BXD69\":\"6.548\",\"BXD70\":\"6.520\",\"BXD71\":\"x\",\"BXD72\":\"x\",\"BXD73\":\"6.484\",\"BXD73a\":\"6.486\",\"BXD73b\":\"x\",\"BXD74\":\"6.639\",\"BXD75\":\"6.401\",\"BXD76\":\"6.452\",\"BXD77\":\"6.568\",\"BXD78\":\"x\",\"BXD79\":\"6.642\",\"BXD81\":\"x\",\"BXD83\":\"6.446\",\"BXD84\":\"6.582\",\"BXD85\":\"6.484\",\"BXD86\":\"6.877\",\"BXD87\":\"6.474\",\"BXD88\":\"x\",\"BXD89\":\"6.676\",\"BXD90\":\"6.644\",\"BXD91\":\"x\",\"BXD93\":\"6.620\",\"BXD94\":\"6.528\",\"BXD95\":\"x\",\"BXD98\":\"6.486\",\"BXD99\":\"6.530\",\"BXD100\":\"x\",\"BXD101\":\"x\",\"BXD102\":\"x\",\"BXD104\":\"x\",\"BXD105\":\"x\",\"BXD106\":\"x\",\"BXD107\":\"x\",\"BXD108\":\"x\",\"BXD109\":\"x\",\"BXD110\":\"x\",\"BXD111\":\"x\",\"BXD112\":\"x\",\"BXD113\":\"x\",\"BXD114\":\"x\",\"BXD115\":\"x\",\"BXD116\":\"x\",\"BXD117\":\"x\",\"BXD119\":\"x\",\"BXD120\":\"x\",\"BXD121\":\"x\",\"BXD122\":\"x\",\"BXD123\":\"x\",\"BXD124\":\"x\",\"BXD125\":\"x\",\"BXD126\":\"x\",\"BXD127\":\"x\",\"BXD128\":\"x\",\"BXD128a\":\"x\",\"BXD130\":\"x\",\"BXD131\":\"x\",\"BXD132\":\"x\",\"BXD133\":\"x\",\"BXD134\":\"x\",\"BXD135\":\"x\",\"BXD136\":\"x\",\"BXD137\":\"x\",\"BXD138\":\"x\",\"BXD139\":\"x\",\"BXD141\":\"x\",\"BXD142\":\"x\",\"BXD144\":\"x\",\"BXD145\":\"x\",\"BXD146\":\"x\",\"BXD147\":\"x\",\"BXD148\":\"x\",\"BXD149\":\"x\",\"BXD150\":\"x\",\"BXD151\":\"x\",\"BXD152\":\"x\",\"BXD153\":\"x\",\"BXD154\":\"x\",\"BXD155\":\"x\",\"BXD156\":\"x\",\"BXD157\":\"x\",\"BXD160\":\"x\",\"BXD161\":\"x\",\"BXD162\":\"x\",\"BXD165\":\"x\",\"BXD168\":\"x\",\"BXD169\":\"x\",\"BXD170\":\"x\",\"BXD171\":\"x\",\"BXD172\":\"x\",\"BXD173\":\"x\",\"BXD174\":\"x\",\"BXD175\":\"x\",\"BXD176\":\"x\",\"BXD177\":\"x\",\"BXD178\":\"x\",\"BXD180\":\"x\",\"BXD181\":\"x\",\"BXD183\":\"x\",\"BXD184\":\"x\",\"BXD186\":\"x\",\"BXD187\":\"x\",\"BXD188\":\"x\",\"BXD189\":\"x\",\"BXD190\":\"x\",\"BXD191\":\"x\",\"BXD192\":\"x\",\"BXD193\":\"x\",\"BXD194\":\"x\",\"BXD195\":\"x\",\"BXD196\":\"x\",\"BXD197\":\"x\",\"BXD198\":\"x\",\"BXD199\":\"x\",\"BXD200\":\"x\",\"BXD201\":\"x\",\"BXD202\":\"x\",\"BXD203\":\"x\",\"BXD204\":\"x\",\"BXD205\":\"x\",\"BXD206\":\"x\",\"BXD207\":\"x\",\"BXD208\":\"x\",\"BXD209\":\"x\",\"BXD210\":\"x\",\"BXD211\":\"x\",\"BXD212\":\"x\",\"BXD213\":\"x\",\"BXD214\":\"x\",\"BXD215\":\"x\",\"BXD216\":\"x\",\"BXD217\":\"x\",\"BXD218\":\"x\",\"BXD219\":\"x\",\"BXD220\":\"x\"}",
- "corr_type": "lit",
- "corr_dataset": "HC_M2_0606_P",
- "corr_return_results": "100",
- "corr_samples_group": "samples_primary",
- "corr_sample_method": "pearson",
- "min_expr": "",
- "location_type": "gene",
- "loc_chr": "",
- "min_loc_mb": "",
- "max_loc_mb": "",
- "p_range_lower": "-0.60",
- "p_range_upper": "0.74"
-} \ No newline at end of file
diff --git a/tests/unit/correlation/dataset.json b/tests/unit/correlation/dataset.json
deleted file mode 100644
index 8a53ed5..0000000
--- a/tests/unit/correlation/dataset.json
+++ /dev/null
@@ -1,64 +0,0 @@
-{
- "name":"HC_M2_0606_P",
- "id":112,
- "shortname":"Hippocampus M430v2 BXD 06/06 PDNN",
- "fullname":"Hippocampus Consortium M430v2 (Jun06) PDNN",
- "type":"ProbeSet",
- "data_scale":"log2",
- "search_fields":[
- "Name",
- "Description",
- "Probe_Target_Description",
- "Symbol",
- "Alias",
- "GenbankId",
- "UniGeneId",
- "RefSeq_TranscriptId"
- ],
- "display_fields":[
- "name",
- "symbol",
- "description",
- "probe_target_description",
- "chr",
- "mb",
- "alias",
- "geneid",
- "genbankid",
- "unigeneid",
- "omim",
- "refseq_transcriptid",
- "blatseq",
- "targetseq",
- "chipid",
- "comments",
- "strand_probe",
- "strand_gene",
- "proteinid",
- "uniprotid",
- "probe_set_target_region",
- "probe_set_specificity",
- "probe_set_blat_score",
- "probe_set_blat_mb_start",
- "probe_set_blat_mb_end",
- "probe_set_strand",
- "probe_set_note_by_rw",
- "flag"
- ],
- "header_fields":[
- "Index",
- "Record",
- "Symbol",
- "Description",
- "Location",
- "Mean",
- "Max LRS",
- "Max LRS Location",
- "Additive Effect"
- ],
- "query_for_group":"\n SELECT\n InbredSet.Name, InbredSet.Id, InbredSet.GeneticType\n FROM\n InbredSet, ProbeSetFreeze, ProbeFreeze\n WHERE\n ProbeFreeze.InbredSetId = InbredSet.Id AND\n ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND\n ProbeSetFreeze.Name = \"HC_M2_0606_P\"\n ",
- "tissue":"Hippocampus mRNA",
- "group":"None",
- "accession_id":"None",
- "species":"None"
-} \ No newline at end of file
diff --git a/tests/unit/correlation/expected_correlation_results.json b/tests/unit/correlation/expected_correlation_results.json
deleted file mode 100644
index b5bbc2d..0000000
--- a/tests/unit/correlation/expected_correlation_results.json
+++ /dev/null
@@ -1,1902 +0,0 @@
-[
- {
- "index": 1,
- "trait_id": "1415758_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415758_at:HC_M2_0606_P:da50fa1141a7d608ab20",
- "symbol": "Fryl",
- "description": "furry homolog-like; far 3' UTR",
- "location": "Chr5: 72.964984",
- "mean": "9.193",
- "additive": "-0.081",
- "lod_score": "4.4",
- "lrs_location": "Chr1: 196.404284",
- "sample_r": "-0.407",
- "num_overlap": 67,
- "sample_p": "6.234e-04",
- "lit_corr": "--",
- "tissue_corr": "-0.221",
- "tissue_pvalue": "2.780e-01"
- },
- {
- "index": 2,
- "trait_id": "1415693_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415693_at:HC_M2_0606_P:0959e913366f559ea22b",
- "symbol": "Derl1",
- "description": "derlin 1; proximal to mid 3' UTR",
- "location": "Chr15: 57.702171",
- "mean": "9.445",
- "additive": "0.056",
- "lod_score": "2.1",
- "lrs_location": "Chr1: 193.731996",
- "sample_r": "0.398",
- "num_overlap": 67,
- "sample_p": "8.614e-04",
- "lit_corr": "--",
- "tissue_corr": "0.114",
- "tissue_pvalue": "5.800e-01"
- },
- {
- "index": 3,
- "trait_id": "1415753_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415753_at:HC_M2_0606_P:d75ca42e7fa1613364bb",
- "symbol": "Fam108a",
- "description": "abhydrolase domain-containing protein FAM108A; last two exons and proximal 3' UTR",
- "location": "Chr10: 80.046470",
- "mean": "12.731",
- "additive": "0.050",
- "lod_score": "1.5",
- "lrs_location": "ChrX: 103.404884",
- "sample_r": "0.384",
- "num_overlap": 67,
- "sample_p": "1.344e-03",
- "lit_corr": "--",
- "tissue_corr": "0.108",
- "tissue_pvalue": "5.990e-01"
- },
- {
- "index": 4,
- "trait_id": "1415740_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415740_at:HC_M2_0606_P:755cdc41d0d50a03b647",
- "symbol": "Psmc5",
- "description": "protease (prosome, macropain) 26S subunit, ATPase 5; exons 7, 8, 9",
- "location": "Chr11: 106.123450",
- "mean": "12.424",
- "additive": "0.059",
- "lod_score": "2.6",
- "lrs_location": "Chr9: 34.013550",
- "sample_r": "0.364",
- "num_overlap": 67,
- "sample_p": "2.476e-03",
- "lit_corr": "--",
- "tissue_corr": "0.333",
- "tissue_pvalue": "9.696e-02"
- },
- {
- "index": 5,
- "trait_id": "1415757_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415757_at:HC_M2_0606_P:8bbf06aa2e3aa5530934",
- "symbol": "Gbf1",
- "description": "Golgi-specific brefeldin A-resistance factor 1; last exon and proximal 3' UTR",
- "location": "Chr19: 46.360410",
- "mean": "9.800",
- "additive": "-0.062",
- "lod_score": "2.0",
- "lrs_location": "Chr17: 52.750885",
- "sample_r": "0.363",
- "num_overlap": 67,
- "sample_p": "2.539e-03",
- "lit_corr": "--",
- "tissue_corr": "-0.059",
- "tissue_pvalue": "7.741e-01"
- },
- {
- "index": 6,
- "trait_id": "1415768_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415768_a_at:HC_M2_0606_P:5e67109eee04f5da3393",
- "symbol": "Ube2r2",
- "description": "ubiquitin-conjugating enzyme E2R 2",
- "location": "Chr4: 41.137929",
- "mean": "9.811",
- "additive": "-0.087",
- "lod_score": "3.3",
- "lrs_location": "Chr12: 114.553844",
- "sample_r": "-0.312",
- "num_overlap": 67,
- "sample_p": "1.019e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.007",
- "tissue_pvalue": "9.711e-01"
- },
- {
- "index": 7,
- "trait_id": "1415670_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415670_at:HC_M2_0606_P:4f82d7374f29ebfacaaf",
- "symbol": "Copg",
- "description": "coatomer protein complex, subunit gamma 1; two of the three last exons and proximal 3' UTR",
- "location": "Chr6: 87.859681",
- "mean": "11.199",
- "additive": "-0.113",
- "lod_score": "3.7",
- "lrs_location": "Chr1: 157.588921",
- "sample_r": "0.305",
- "num_overlap": 67,
- "sample_p": "1.200e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.405",
- "tissue_pvalue": "4.032e-02"
- },
- {
- "index": 8,
- "trait_id": "1415742_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415742_at:HC_M2_0606_P:b72a582a1f840a18c3e7",
- "symbol": "Aup1",
- "description": "ancient ubiquitous protein 1",
- "location": "Chr6: 83.006784",
- "mean": "9.529",
- "additive": "-0.062",
- "lod_score": "2.4",
- "lrs_location": "Chr19: 16.955950",
- "sample_r": "0.295",
- "num_overlap": 67,
- "sample_p": "1.523e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.033",
- "tissue_pvalue": "8.716e-01"
- },
- {
- "index": 9,
- "trait_id": "1415743_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415743_at:HC_M2_0606_P:3187245a079e824b4236",
- "symbol": "Hdac5",
- "description": "histone deacetylase 5; last four exons",
- "location": "Chr11: 102.057397",
- "mean": "11.009",
- "additive": "0.081",
- "lod_score": "2.1",
- "lrs_location": "Chr7: 125.263073",
- "sample_r": "0.285",
- "num_overlap": 67,
- "sample_p": "1.950e-02",
- "lit_corr": "--",
- "tissue_corr": "0.005",
- "tissue_pvalue": "9.823e-01"
- },
- {
- "index": 10,
- "trait_id": "1415690_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415690_at:HC_M2_0606_P:603b215ede00b6fe1104",
- "symbol": "Mrp127",
- "description": "39S ribosomal protein L27, mitochondrial; last three exons",
- "location": "Chr11: 94.517922",
- "mean": "12.569",
- "additive": "0.063",
- "lod_score": "1.9",
- "lrs_location": "Chr2: 164.779024",
- "sample_r": "0.266",
- "num_overlap": 67,
- "sample_p": "2.986e-02",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 11,
- "trait_id": "1415727_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415727_at:HC_M2_0606_P:cb40b8cba0eee75781a6",
- "symbol": "Apoa1bp",
- "description": "apolipoprotein A-I binding protein; exons 3 through 6",
- "location": "Chr3: 87.860534",
- "mean": "11.707",
- "additive": "-0.076",
- "lod_score": "2.8",
- "lrs_location": "Chr3: 56.295375",
- "sample_r": "0.263",
- "num_overlap": 67,
- "sample_p": "3.136e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.535",
- "tissue_pvalue": "4.841e-03"
- },
- {
- "index": 12,
- "trait_id": "1415730_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415730_at:HC_M2_0606_P:a970e0610a56ac4aba27",
- "symbol": "Cpsf7",
- "description": "cleavage and polyadenylation specificity factor 7; distal 3' UTR (transQTL on Chr 4 in BXD eye data)",
- "location": "Chr19: 10.621618",
- "mean": "10.662",
- "additive": "-0.048",
- "lod_score": "2.1",
- "lrs_location": "Chr1: 188.085707",
- "sample_r": "-0.263",
- "num_overlap": 67,
- "sample_p": "3.164e-02",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 13,
- "trait_id": "1415741_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415741_at:HC_M2_0606_P:033752be361d32960c29",
- "symbol": "Tmem165",
- "description": "transmembrane protein 165; 3' UTR",
- "location": "Chr5: 76.637708",
- "mean": "10.974",
- "additive": "0.048",
- "lod_score": "2.0",
- "lrs_location": "Chr4: 5.606394",
- "sample_r": "-0.258",
- "num_overlap": 67,
- "sample_p": "3.489e-02",
- "lit_corr": "--",
- "tissue_corr": "0.271",
- "tissue_pvalue": "1.812e-01"
- },
- {
- "index": 14,
- "trait_id": "1415725_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415725_at:HC_M2_0606_P:fbd6458be4f8ccbf1dc0",
- "symbol": "Rrn3",
- "description": "RRN3 RNA polymerase I transcription factor homolog (yeast)",
- "location": "Chr16: 13.814359",
- "mean": "9.195",
- "additive": "-0.085",
- "lod_score": "2.8",
- "lrs_location": "Chr1: 148.717644",
- "sample_r": "0.256",
- "num_overlap": 67,
- "sample_p": "3.636e-02",
- "lit_corr": "--",
- "tissue_corr": "0.587",
- "tissue_pvalue": "1.621e-03"
- },
- {
- "index": 15,
- "trait_id": "1415717_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415717_at:HC_M2_0606_P:dd51438830e4033114f8",
- "symbol": "Rnf220",
- "description": "ring finger protein 220; mid 3' UTR",
- "location": "Chr4: 116.944155",
- "mean": "10.778",
- "additive": "-0.084",
- "lod_score": "2.4",
- "lrs_location": "Chr4: 122.536808",
- "sample_r": "0.242",
- "num_overlap": 67,
- "sample_p": "4.816e-02",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 16,
- "trait_id": "1415703_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415703_at:HC_M2_0606_P:51ee8e47654845a546f0",
- "symbol": "Huwe1",
- "description": "HECT, UBA and WWE domain containing 1; last 3 exons and proximal 3' UTR",
- "location": "ChrX: 148.367136",
- "mean": "11.335",
- "additive": "-0.094",
- "lod_score": "2.3",
- "lrs_location": "Chr1: 135.891043",
- "sample_r": "0.235",
- "num_overlap": 67,
- "sample_p": "5.541e-02",
- "lit_corr": "--",
- "tissue_corr": "0.528",
- "tissue_pvalue": "5.576e-03"
- },
- {
- "index": 17,
- "trait_id": "1415748_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415748_a_at:HC_M2_0606_P:749a2279081b54e89885",
- "symbol": "Dctn5",
- "description": "dynactin 5; last exon and proximal half of 3' UTR",
- "location": "Chr7: 129.291923",
- "mean": "11.250",
- "additive": "0.071",
- "lod_score": "3.4",
- "lrs_location": "Chr5: 138.337847",
- "sample_r": "0.230",
- "num_overlap": 67,
- "sample_p": "6.133e-02",
- "lit_corr": "--",
- "tissue_corr": "0.064",
- "tissue_pvalue": "7.557e-01"
- },
- {
- "index": 18,
- "trait_id": "1415706_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415706_at:HC_M2_0606_P:ddfffdb78d0ff84d6a1a",
- "symbol": "Copa",
- "description": "coatomer protein complex, subunit alpha; 3' UTR",
- "location": "Chr1: 174.051912",
- "mean": "12.577",
- "additive": "-0.143",
- "lod_score": "8.7",
- "lrs_location": "Chr1: 172.981863",
- "sample_r": "0.224",
- "num_overlap": 67,
- "sample_p": "6.829e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.147",
- "tissue_pvalue": "4.739e-01"
- },
- {
- "index": 19,
- "trait_id": "1415696_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415696_at:HC_M2_0606_P:da00b2667d7c27dc76a2",
- "symbol": "Sar1a",
- "description": "SAR1 gene homolog A; distal 3' UTR",
- "location": "Chr10: 61.155492",
- "mean": "11.447",
- "additive": "-0.051",
- "lod_score": "2.4",
- "lrs_location": "Chr15: 87.788313",
- "sample_r": "0.220",
- "num_overlap": 67,
- "sample_p": "7.356e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.559",
- "tissue_pvalue": "3.015e-03"
- },
- {
- "index": 20,
- "trait_id": "1415731_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415731_at:HC_M2_0606_P:9e91e97ca1001091a5f3",
- "symbol": "Angel2",
- "description": "angel homolog 2; distal 3' UTR",
- "location": "Chr1: 192.769800",
- "mean": "9.490",
- "additive": "0.062",
- "lod_score": "2.6",
- "lrs_location": "Chr14: 124.508018",
- "sample_r": "0.218",
- "num_overlap": 67,
- "sample_p": "7.623e-02",
- "lit_corr": "--",
- "tissue_corr": "0.232",
- "tissue_pvalue": "2.544e-01"
- },
- {
- "index": 21,
- "trait_id": "1415750_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415750_at:HC_M2_0606_P:c9f757736d57e5f23aa5",
- "symbol": "Tbl3",
- "description": "transducin (beta)-like 3",
- "location": "Chr17: 24.838067",
- "mean": "8.703",
- "additive": "-0.132",
- "lod_score": "10.0",
- "lrs_location": "Chr17: 23.322636",
- "sample_r": "0.213",
- "num_overlap": 67,
- "sample_p": "8.332e-02",
- "lit_corr": "--",
- "tissue_corr": "0.312",
- "tissue_pvalue": "1.211e-01"
- },
- {
- "index": 22,
- "trait_id": "1415680_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415680_at:HC_M2_0606_P:22e90a54261cb373975e",
- "symbol": "Anapc1",
- "description": "anaphase promoting complex subunit 1; last 3 exons and 3' UTR",
- "location": "Chr2: 128.438499",
- "mean": "9.180",
- "additive": "-0.102",
- "lod_score": "8.7",
- "lrs_location": "Chr2: 125.304784",
- "sample_r": "-0.210",
- "num_overlap": 67,
- "sample_p": "8.734e-02",
- "lit_corr": "--",
- "tissue_corr": "0.367",
- "tissue_pvalue": "6.539e-02"
- },
- {
- "index": 23,
- "trait_id": "1415712_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415712_at:HC_M2_0606_P:48e284402cb79a5fbede",
- "symbol": "Zranb1",
- "description": "zinc finger, RAN-binding domain containing 1 (ubiquitin thioesterase, TRAF-binding protein); far 3' UTR (M430AB control duplicate)",
- "location": "Chr7: 140.175988",
- "mean": "9.923",
- "additive": "-0.079",
- "lod_score": "2.8",
- "lrs_location": "Chr5: 143.642242",
- "sample_r": "-0.208",
- "num_overlap": 67,
- "sample_p": "9.125e-02",
- "lit_corr": "--",
- "tissue_corr": "-0.068",
- "tissue_pvalue": "7.413e-01"
- },
- {
- "index": 24,
- "trait_id": "1415674_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415674_a_at:HC_M2_0606_P:c8e7fb1fcad21d73fcfd",
- "symbol": "Trappc4",
- "description": "trafficking protein particle complex 4; exons 3 and 4",
- "location": "Chr9: 44.212489",
- "mean": "10.760",
- "additive": "-0.065",
- "lod_score": "3.3",
- "lrs_location": "Chr5: 69.527298",
- "sample_r": "0.201",
- "num_overlap": 67,
- "sample_p": "1.028e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.334",
- "tissue_pvalue": "9.587e-02"
- },
- {
- "index": 25,
- "trait_id": "1415747_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415747_s_at:HC_M2_0606_P:5d86584be55f6cec47ab",
- "symbol": "Riok3",
- "description": "RIO kinase 3 (yeast); mid to distal 3' UTR",
- "location": "Chr18: 12.314783",
- "mean": "10.906",
- "additive": "0.068",
- "lod_score": "2.1",
- "lrs_location": "Chr4: 13.764991",
- "sample_r": "-0.198",
- "num_overlap": 67,
- "sample_p": "1.081e-01",
- "lit_corr": "--",
- "tissue_corr": "0.282",
- "tissue_pvalue": "1.628e-01"
- },
- {
- "index": 26,
- "trait_id": "1415682_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415682_at:HC_M2_0606_P:d02febdf17a279a71088",
- "symbol": "Xpo7",
- "description": "exportin 7",
- "location": "Chr14: 71.064730",
- "mean": "9.075",
- "additive": "-0.073",
- "lod_score": "2.8",
- "lrs_location": "Chr17: 68.421021",
- "sample_r": "0.197",
- "num_overlap": 67,
- "sample_p": "1.092e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.322",
- "tissue_pvalue": "1.084e-01"
- },
- {
- "index": 27,
- "trait_id": "1415732_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415732_at:HC_M2_0606_P:c0010f5b42f210874883",
- "symbol": "Abhd16a",
- "description": "abhydrolase domain containing 16A; last five exons including proximal 3' UTR",
- "location": "Chr17: 35.238940",
- "mean": "10.798",
- "additive": "-0.132",
- "lod_score": "6.1",
- "lrs_location": "Chr17: 37.015392",
- "sample_r": "0.177",
- "num_overlap": 67,
- "sample_p": "1.527e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 28,
- "trait_id": "1415688_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415688_at:HC_M2_0606_P:4c3b6c7cd3d447f2346c",
- "symbol": "Ube2g1",
- "description": "ubiquitin-conjugating enzyme E2 G1; mid to distal 3' UTR",
- "location": "Chr11: 72.497627",
- "mean": "11.494",
- "additive": "-0.116",
- "lod_score": "7.1",
- "lrs_location": "Chr11: 72.486317",
- "sample_r": "-0.173",
- "num_overlap": 67,
- "sample_p": "1.605e-01",
- "lit_corr": "--",
- "tissue_corr": "0.365",
- "tissue_pvalue": "6.671e-02"
- },
- {
- "index": 29,
- "trait_id": "1415698_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415698_at:HC_M2_0606_P:4d8988a8fac8bdbce9c2",
- "symbol": "Golm1",
- "description": "Golgi membrane protein 1; distal 3' UTR",
- "location": "Chr13: 59.736417",
- "mean": "11.367",
- "additive": "0.113",
- "lod_score": "2.9",
- "lrs_location": "Chr7: 36.124856",
- "sample_r": "0.151",
- "num_overlap": 67,
- "sample_p": "2.221e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.053",
- "tissue_pvalue": "7.958e-01"
- },
- {
- "index": 30,
- "trait_id": "1415697_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415697_at:HC_M2_0606_P:ab18358c61fbc03fdf13",
- "symbol": "G3bp2",
- "description": "GTPase activating protein (SH3 domain) binding protein 2; mid proximal 3' UTR",
- "location": "Chr5: 92.482845",
- "mean": "10.768",
- "additive": "0.137",
- "lod_score": "3.6",
- "lrs_location": "Chr5: 138.337847",
- "sample_r": "0.142",
- "num_overlap": 67,
- "sample_p": "2.504e-01",
- "lit_corr": "--",
- "tissue_corr": "0.107",
- "tissue_pvalue": "6.032e-01"
- },
- {
- "index": 31,
- "trait_id": "1415676_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415676_a_at:HC_M2_0606_P:b236ce0b2af4408662b6",
- "symbol": "Psmb5",
- "description": "proteasome (prosome, macropain) subunit, beta type 5; coding exons 2 and 3",
- "location": "Chr14: 55.233131",
- "mean": "14.199",
- "additive": "0.130",
- "lod_score": "6.9",
- "lrs_location": "Chr14: 54.987777",
- "sample_r": "-0.136",
- "num_overlap": 67,
- "sample_p": "2.725e-01",
- "lit_corr": "--",
- "tissue_corr": "0.152",
- "tissue_pvalue": "4.580e-01"
- },
- {
- "index": 32,
- "trait_id": "1415723_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415723_at:HC_M2_0606_P:8672294efc1c30e220c2",
- "symbol": "Eif5",
- "description": "eukaryotic translation initiation factor 5; distal 3' UTR",
- "location": "Chr12: 112.784258",
- "mean": "12.507",
- "additive": "-0.196",
- "lod_score": "12.9",
- "lrs_location": "Chr12: 112.426348",
- "sample_r": "-0.134",
- "num_overlap": 67,
- "sample_p": "2.795e-01",
- "lit_corr": "--",
- "tissue_corr": "0.105",
- "tissue_pvalue": "6.104e-01"
- },
- {
- "index": 33,
- "trait_id": "1415692_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415692_s_at:HC_M2_0606_P:a30c9243d16dd6d28826",
- "symbol": "Canx",
- "description": "calnexin; mid 3' UTR",
- "location": "Chr11: 50.108505",
- "mean": "13.862",
- "additive": "0.090",
- "lod_score": "3.3",
- "lrs_location": "Chr9: 15.693672",
- "sample_r": "0.133",
- "num_overlap": 67,
- "sample_p": "2.828e-01",
- "lit_corr": "--",
- "tissue_corr": "0.298",
- "tissue_pvalue": "1.388e-01"
- },
- {
- "index": 34,
- "trait_id": "1415728_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415728_at:HC_M2_0606_P:449a770634eff3bac9f5",
- "symbol": "Pabpn1",
- "description": "polyadenylate-binding protein 2; far 3' UTR",
- "location": "Chr14: 55.517242",
- "mean": "10.510",
- "additive": "0.150",
- "lod_score": "2.3",
- "lrs_location": "Chr19: 53.933992",
- "sample_r": "-0.130",
- "num_overlap": 67,
- "sample_p": "2.942e-01",
- "lit_corr": "--",
- "tissue_corr": "0.132",
- "tissue_pvalue": "5.194e-01"
- },
- {
- "index": 35,
- "trait_id": "1415675_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415675_at:HC_M2_0606_P:9712db695d534370b0d9",
- "symbol": "Dpm2",
- "description": "dolichol-phosphate (beta-D) mannosyltransferase 2; last exon and proximal to mid 3' UTR",
- "location": "Chr2: 32.428524",
- "mean": "10.207",
- "additive": "-0.043",
- "lod_score": "2.6",
- "lrs_location": "Chr13: 30.769380",
- "sample_r": "-0.129",
- "num_overlap": 67,
- "sample_p": "2.966e-01",
- "lit_corr": "--",
- "tissue_corr": "0.102",
- "tissue_pvalue": "6.201e-01"
- },
- {
- "index": 36,
- "trait_id": "1415721_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415721_a_at:HC_M2_0606_P:fd804230fcc3400d6b4b",
- "symbol": "Naa60",
- "description": "N(alpha)-acetyltransferase 60, NatF catalytic subunit; distal 3' UTR",
- "location": "Chr16: 3.904169",
- "mean": "10.153",
- "additive": "-0.059",
- "lod_score": "3.6",
- "lrs_location": "Chr2: 159.368724",
- "sample_r": "0.128",
- "num_overlap": 67,
- "sample_p": "3.004e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 37,
- "trait_id": "1415733_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415733_a_at:HC_M2_0606_P:4eff33f3ecd4c0dd418e",
- "symbol": "Shb",
- "description": "Src homology 2 domain containing adaptor protein B; putative far 3' UTR (or intercalated neighbor)",
- "location": "Chr4: 45.118127",
- "mean": "10.756",
- "additive": "-0.044",
- "lod_score": "1.9",
- "lrs_location": "Chr5: 69.527298",
- "sample_r": "0.126",
- "num_overlap": 67,
- "sample_p": "3.103e-01",
- "lit_corr": "--",
- "tissue_corr": "0.149",
- "tissue_pvalue": "4.678e-01"
- },
- {
- "index": 38,
- "trait_id": "1415720_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415720_s_at:HC_M2_0606_P:4e7dab211ec586e8297a",
- "symbol": "Mad2l1bp",
- "description": "mitotic arrest deficient 2, homolog-like 1 (MAD2L1) binding protein; last exon and 3' UTR",
- "location": "Chr17: 46.284624",
- "mean": "7.057",
- "additive": "0.048",
- "lod_score": "2.5",
- "lrs_location": "Chr8: 33.934048",
- "sample_r": "0.122",
- "num_overlap": 67,
- "sample_p": "3.262e-01",
- "lit_corr": "--",
- "tissue_corr": "0.463",
- "tissue_pvalue": "1.709e-02"
- },
- {
- "index": 39,
- "trait_id": "1415767_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415767_at:HC_M2_0606_P:3e5a802a95121f3ffa1f",
- "symbol": "Ythdf1",
- "description": "YTH domain family, member 1; mid 3' UTR",
- "location": "Chr2: 180.639551",
- "mean": "10.902",
- "additive": "-0.051",
- "lod_score": "2.2",
- "lrs_location": "Chr6: 145.406059",
- "sample_r": "-0.120",
- "num_overlap": 67,
- "sample_p": "3.325e-01",
- "lit_corr": "--",
- "tissue_corr": "0.382",
- "tissue_pvalue": "5.396e-02"
- },
- {
- "index": 40,
- "trait_id": "1415762_x_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415762_x_at:HC_M2_0606_P:978ad700958782192aa2",
- "symbol": "Mrpl52",
- "description": "mitochondrial ribosomal protein L52",
- "location": "Chr14: 55.045789",
- "mean": "10.926",
- "additive": "0.086",
- "lod_score": "2.5",
- "lrs_location": "Chr1: 190.087097",
- "sample_r": "0.118",
- "num_overlap": 67,
- "sample_p": "3.406e-01",
- "lit_corr": "--",
- "tissue_corr": "0.395",
- "tissue_pvalue": "4.585e-02"
- },
- {
- "index": 41,
- "trait_id": "1415736_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415736_at:HC_M2_0606_P:c9bd62acd0c2cc087606",
- "symbol": "Pfdn5",
- "description": "prefoldin 5",
- "location": "Chr15: 102.156651",
- "mean": "13.571",
- "additive": "0.095",
- "lod_score": "2.3",
- "lrs_location": "Chr10: 5.378622",
- "sample_r": "0.118",
- "num_overlap": 67,
- "sample_p": "3.418e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.261",
- "tissue_pvalue": "1.975e-01"
- },
- {
- "index": 42,
- "trait_id": "1415704_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415704_a_at:HC_M2_0606_P:a05982c0214ff2dc2a40",
- "symbol": "Cdv3",
- "description": "carnitine deficiency-associated gene expressed in ventricle 3",
- "location": "Chr9: 103.255487",
- "mean": "10.994",
- "additive": "0.060",
- "lod_score": "3.1",
- "lrs_location": "Chr3: 10.018672",
- "sample_r": "-0.115",
- "num_overlap": 67,
- "sample_p": "3.539e-01",
- "lit_corr": "--",
- "tissue_corr": "0.598",
- "tissue_pvalue": "1.246e-03"
- },
- {
- "index": 43,
- "trait_id": "1415699_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415699_a_at:HC_M2_0606_P:8a5c52aea60cad17e29c",
- "symbol": "Gps1",
- "description": "G protein pathway suppressor 1 (COP9 signalosome complex subunit 1)",
- "location": "Chr11: 120.649820",
- "mean": "12.033",
- "additive": "0.065",
- "lod_score": "3.4",
- "lrs_location": "Chr11: 62.910461",
- "sample_r": "-0.114",
- "num_overlap": 67,
- "sample_p": "3.575e-01",
- "lit_corr": "--",
- "tissue_corr": "0.150",
- "tissue_pvalue": "4.638e-01"
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- {
- "index": 44,
- "trait_id": "1415739_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415739_at:HC_M2_0606_P:c5e8b34713057f53dd07",
- "symbol": "Rbm42",
- "description": "RNA-binding motif protein 42; exon 7 and 3' UTR",
- "location": "Chr7: 31.426055",
- "mean": "10.926",
- "additive": "-0.154",
- "lod_score": "12.8",
- "lrs_location": "Chr1: 174.792334",
- "sample_r": "0.107",
- "num_overlap": 67,
- "sample_p": "3.898e-01",
- "lit_corr": "--",
- "tissue_corr": "0.550",
- "tissue_pvalue": "3.580e-03"
- },
- {
- "index": 45,
- "trait_id": "1415695_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415695_at:HC_M2_0606_P:44556cafdf6f5e38669b",
- "symbol": "Psma1",
- "description": "proteasome (prosome, macropain) subunit, alpha type 1; last four exons and proximal 3' UTR",
- "location": "Chr7: 121.408358",
- "mean": "12.346",
- "additive": "-0.081",
- "lod_score": "3.1",
- "lrs_location": "Chr12: 29.344230",
- "sample_r": "-0.106",
- "num_overlap": 67,
- "sample_p": "3.925e-01",
- "lit_corr": "--",
- "tissue_corr": "0.274",
- "tissue_pvalue": "1.763e-01"
- },
- {
- "index": 46,
- "trait_id": "1415745_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415745_a_at:HC_M2_0606_P:0178fc19ada3ba0179fb",
- "symbol": "Dscr3",
- "description": "Down syndrome critical region protein 3",
- "location": "Chr16: 94.719451",
- "mean": "9.329",
- "additive": "0.071",
- "lod_score": "2.2",
- "lrs_location": "Chr4: 19.960179",
- "sample_r": "-0.102",
- "num_overlap": 67,
- "sample_p": "4.133e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.138",
- "tissue_pvalue": "5.025e-01"
- },
- {
- "index": 47,
- "trait_id": "1415763_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415763_a_at:HC_M2_0606_P:489dea4b682a7f0b5dc4",
- "symbol": "Tmem234",
- "description": "transmembrane protein 234; far 3' UTR",
- "location": "Chr4: 129.285471",
- "mean": "11.370",
- "additive": "-0.080",
- "lod_score": "2.7",
- "lrs_location": "Chr19: 36.251059",
- "sample_r": "-0.099",
- "num_overlap": 67,
- "sample_p": "4.274e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 48,
- "trait_id": "1415707_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415707_at:HC_M2_0606_P:44193c047da5c37a307d",
- "symbol": "Anapc2",
- "description": "anaphase promoting complex subunit 2; last two exons and proximal 3' UTR",
- "location": "Chr2: 25.140684",
- "mean": "10.044",
- "additive": "0.057",
- "lod_score": "3.0",
- "lrs_location": "Chr11: 76.761051",
- "sample_r": "-0.096",
- "num_overlap": 67,
- "sample_p": "4.378e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.121",
- "tissue_pvalue": "5.551e-01"
- },
- {
- "index": 49,
- "trait_id": "1415716_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415716_a_at:HC_M2_0606_P:c453f863ce1446551a6c",
- "symbol": "Rps27",
- "description": "ribosomal protein S27; last two exons and proximal 3' UTR",
- "location": "Chr3: 90.016627",
- "mean": "15.694",
- "additive": "0.132",
- "lod_score": "3.2",
- "lrs_location": "Chr1: 165.315110",
- "sample_r": "0.092",
- "num_overlap": 67,
- "sample_p": "4.594e-01",
- "lit_corr": "--",
- "tissue_corr": "0.150",
- "tissue_pvalue": "4.654e-01"
- },
- {
- "index": 50,
- "trait_id": "1415769_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415769_at:HC_M2_0606_P:564c4d3bb19aca88c74b",
- "symbol": "Itch",
- "description": "itchy, E3 ubiquitin protein ligase; distal 3' UTR",
- "location": "Chr2: 155.052012",
- "mean": "9.460",
- "additive": "0.057",
- "lod_score": "2.5",
- "lrs_location": "Chr7: 56.652492",
- "sample_r": "0.087",
- "num_overlap": 67,
- "sample_p": "4.833e-01",
- "lit_corr": "--",
- "tissue_corr": "0.373",
- "tissue_pvalue": "6.074e-02"
- },
- {
- "index": 51,
- "trait_id": "1415761_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415761_at:HC_M2_0606_P:744c009738648980b1a3",
- "symbol": "Mrpl52",
- "description": "mitochondrial ribosomal protein L52; all five exons",
- "location": "Chr14: 55.045789",
- "mean": "10.635",
- "additive": "0.099",
- "lod_score": "2.9",
- "lrs_location": "Chr4: 155.235046",
- "sample_r": "0.085",
- "num_overlap": 67,
- "sample_p": "4.953e-01",
- "lit_corr": "--",
- "tissue_corr": "0.395",
- "tissue_pvalue": "4.585e-02"
- },
- {
- "index": 52,
- "trait_id": "1415746_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415746_at:HC_M2_0606_P:fed140f95a21fef772a2",
- "symbol": "Cic",
- "description": "capicua transcriptional repressor",
- "location": "Chr7: 26.078638",
- "mean": "12.178",
- "additive": "-0.115",
- "lod_score": "2.0",
- "lrs_location": "Chr11: 64.909098",
- "sample_r": "-0.082",
- "num_overlap": 67,
- "sample_p": "5.099e-01",
- "lit_corr": "--",
- "tissue_corr": "0.263",
- "tissue_pvalue": "1.949e-01"
- },
- {
- "index": 53,
- "trait_id": "1415759_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415759_a_at:HC_M2_0606_P:a27045c52162a32061e0",
- "symbol": "Hbxip",
- "description": "hepatitis B virus x-interacting protein (binds C-terminus of hepatitis B virus X protein, HBx); last two exons and 3' UTR",
- "location": "Chr3: 107.084847",
- "mean": "11.029",
- "additive": "-0.205",
- "lod_score": "13.4",
- "lrs_location": "Chr3: 108.822022",
- "sample_r": "0.081",
- "num_overlap": 67,
- "sample_p": "5.170e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 54,
- "trait_id": "1415705_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415705_at:HC_M2_0606_P:84786a1fa09230a4b766",
- "symbol": "Smim7",
- "description": "small integral membrane protein 7",
- "location": "Chr8: 75.089847",
- "mean": "10.144",
- "additive": "-0.106",
- "lod_score": "4.3",
- "lrs_location": "Chr1: 172.981863",
- "sample_r": "-0.070",
- "num_overlap": 67,
- "sample_p": "5.723e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 55,
- "trait_id": "1415708_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415708_at:HC_M2_0606_P:4c91e4736226606aa737",
- "symbol": "Tug1",
- "description": "taurine upregulated gene 1; distal 3' UTR",
- "location": "Chr11: 3.540066",
- "mean": "11.596",
- "additive": "-0.093",
- "lod_score": "4.0",
- "lrs_location": "Chr6: 145.406059",
- "sample_r": "-0.070",
- "num_overlap": 67,
- "sample_p": "5.733e-01",
- "lit_corr": "--",
- "tissue_corr": "0.612",
- "tissue_pvalue": "8.850e-04"
- },
- {
- "index": 56,
- "trait_id": "1415766_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415766_at:HC_M2_0606_P:204ca6dc37a14c02d1c5",
- "symbol": "Sec22l1",
- "description": "SEC22 vesicle trafficking protein-like 1; distal 3' UTR",
- "location": "Chr3: 97.726622",
- "mean": "10.619",
- "additive": "0.055",
- "lod_score": "2.0",
- "lrs_location": "Chr1: 183.936095",
- "sample_r": "0.070",
- "num_overlap": 67,
- "sample_p": "5.757e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 57,
- "trait_id": "1415722_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415722_a_at:HC_M2_0606_P:c5fd27526c57d8c3fd4b",
- "symbol": "Vta1",
- "description": "Vps20-associated 1; last two exons and proximal 3' UTR",
- "location": "Chr10: 14.375393",
- "mean": "10.716",
- "additive": "-0.076",
- "lod_score": "6.1",
- "lrs_location": "Chr10: 5.378622",
- "sample_r": "0.065",
- "num_overlap": 67,
- "sample_p": "6.012e-01",
- "lit_corr": "--",
- "tissue_corr": "0.421",
- "tissue_pvalue": "3.209e-02"
- },
- {
- "index": 58,
- "trait_id": "1415689_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415689_s_at:HC_M2_0606_P:a70dcbef5742da689bc1",
- "symbol": "Zkscan3",
- "description": "zinc finger with KRAB and SCAN domains 3 (human ZKSCAN4); mid 3' UTR",
- "location": "Chr13: 21.479302",
- "mean": "8.611",
- "additive": "0.064",
- "lod_score": "1.9",
- "lrs_location": "Chr4: 154.365177",
- "sample_r": "-0.064",
- "num_overlap": 67,
- "sample_p": "6.046e-01",
- "lit_corr": "--",
- "tissue_corr": "0.552",
- "tissue_pvalue": "3.454e-03"
- },
- {
- "index": 59,
- "trait_id": "1415754_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415754_at:HC_M2_0606_P:e5bf579fd7db6c886098",
- "symbol": "Polr2f",
- "description": "polymerase (RNA) II (DNA directed) polypeptide F; 5' UTR and exons 1, 2, and 4",
- "location": "Chr15: 78.971834",
- "mean": "10.742",
- "additive": "0.058",
- "lod_score": "2.4",
- "lrs_location": "Chr1: 189.435367",
- "sample_r": "0.062",
- "num_overlap": 67,
- "sample_p": "6.167e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.181",
- "tissue_pvalue": "3.755e-01"
- },
- {
- "index": 60,
- "trait_id": "1415765_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415765_at:HC_M2_0606_P:01b87826e23dea53f4fb",
- "symbol": "Hnrpul2",
- "description": "heterogeneous nuclear ribonucleoprotein U-like 2 (similar to ubiquitin carboxyl-terminal hydrolase 21); 3' UTR",
- "location": "Chr19: 8.905975",
- "mean": "9.165",
- "additive": "-0.091",
- "lod_score": "2.9",
- "lrs_location": "Chr6: 98.258572",
- "sample_r": "-0.061",
- "num_overlap": 67,
- "sample_p": "6.259e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.059",
- "tissue_pvalue": "7.728e-01"
- },
- {
- "index": 61,
- "trait_id": "1415714_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415714_a_at:HC_M2_0606_P:24547c4d8e0d33203c93",
- "symbol": "Snrnp27",
- "description": "small nuclear ribonucleoprotein 27 kDa (U4/U6.U5); exons 3 and 4",
- "location": "Chr6: 86.630900",
- "mean": "12.255",
- "additive": "0.076",
- "lod_score": "3.3",
- "lrs_location": "Chr5: 138.337847",
- "sample_r": "-0.059",
- "num_overlap": 67,
- "sample_p": "6.375e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 62,
- "trait_id": "1415760_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415760_s_at:HC_M2_0606_P:8c46a844ccc841978948",
- "symbol": "Atox1",
- "description": "ATX1 (antioxidant protein 1) homolog 1; last two exons and proximal 3' UTR",
- "location": "Chr11: 55.263981",
- "mean": "11.035",
- "additive": "0.077",
- "lod_score": "1.8",
- "lrs_location": "Chr9: 49.215835",
- "sample_r": "-0.056",
- "num_overlap": 67,
- "sample_p": "6.511e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.243",
- "tissue_pvalue": "2.324e-01"
- },
- {
- "index": 63,
- "trait_id": "1415734_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415734_at:HC_M2_0606_P:aa7f07dc0f541cde5715",
- "symbol": "Rab7",
- "description": "RAB7, member RAS oncogene family (Charcot-Marie-Tooth (CMT) type 2)",
- "location": "Chr6: 87.949145",
- "mean": "13.802",
- "additive": "-0.053",
- "lod_score": "2.3",
- "lrs_location": "Chr1: 172.981863",
- "sample_r": "0.054",
- "num_overlap": 67,
- "sample_p": "6.618e-01",
- "lit_corr": "--",
- "tissue_corr": "0.054",
- "tissue_pvalue": "7.921e-01"
- },
- {
- "index": 64,
- "trait_id": "1415719_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415719_s_at:HC_M2_0606_P:90fe587b88df98f034a9",
- "symbol": "Armc1",
- "description": "armadillo repeat containing 1; distal 3' UTR",
- "location": "Chr3: 19.032212",
- "mean": "11.373",
- "additive": "-0.193",
- "lod_score": "17.0",
- "lrs_location": "Chr3: 19.544553",
- "sample_r": "-0.053",
- "num_overlap": 67,
- "sample_p": "6.680e-01",
- "lit_corr": "--",
- "tissue_corr": "0.305",
- "tissue_pvalue": "1.296e-01"
- },
- {
- "index": 65,
- "trait_id": "1415677_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415677_at:HC_M2_0606_P:0b0c1af1012288383c27",
- "symbol": "Dhrs1",
- "description": "dehydrogenase/reductase (SDR family) member 1; last four exons",
- "location": "Chr14: 56.358423",
- "mean": "10.640",
- "additive": "0.070",
- "lod_score": "4.3",
- "lrs_location": "Chr1: 29.231425",
- "sample_r": "0.052",
- "num_overlap": 67,
- "sample_p": "6.785e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.238",
- "tissue_pvalue": "2.422e-01"
- },
- {
- "index": 66,
- "trait_id": "1415756_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415756_a_at:HC_M2_0606_P:c5252e44b226f6bfb751",
- "symbol": "Snapap",
- "description": "SNAP-associated protein; mid 3' UTR",
- "location": "Chr3: 90.292659",
- "mean": "9.902",
- "additive": "-0.155",
- "lod_score": "9.4",
- "lrs_location": "Chr3: 89.894692",
- "sample_r": "-0.052",
- "num_overlap": 67,
- "sample_p": "6.788e-01",
- "lit_corr": "--",
- "tissue_corr": "0.179",
- "tissue_pvalue": "3.809e-01"
- },
- {
- "index": 67,
- "trait_id": "1415678_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415678_at:HC_M2_0606_P:04b17c5b061ad6e8904b",
- "symbol": "Ppm1a",
- "description": "protein phosphatase 1A, magnesium dependent; 3' UTR",
- "location": "Chr12: 73.894951",
- "mean": "11.586",
- "additive": "-0.075",
- "lod_score": "3.4",
- "lrs_location": "Chr12: 76.396441",
- "sample_r": "-0.051",
- "num_overlap": 67,
- "sample_p": "6.841e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.099",
- "tissue_pvalue": "6.295e-01"
- },
- {
- "index": 68,
- "trait_id": "1415709_s_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415709_s_at:HC_M2_0606_P:4b91fccf51bc6263dcae",
- "symbol": "Gbf1",
- "description": "Golgi-specific brefeldin A-resistance factor 1",
- "location": "Chr19: 46.360511",
- "mean": "9.342",
- "additive": "0.056",
- "lod_score": "3.6",
- "lrs_location": "ChrX: 81.842525",
- "sample_r": "0.050",
- "num_overlap": 67,
- "sample_p": "6.863e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.059",
- "tissue_pvalue": "7.741e-01"
- },
- {
- "index": 69,
- "trait_id": "1415671_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415671_at:HC_M2_0606_P:c3cd4876e293def795bf",
- "symbol": "Atp6v0d1",
- "description": "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1",
- "location": "Chr8: 108.048521",
- "mean": "13.278",
- "additive": "-0.080",
- "lod_score": "3.7",
- "lrs_location": "Chr19: 13.033814",
- "sample_r": "-0.050",
- "num_overlap": 67,
- "sample_p": "6.898e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.284",
- "tissue_pvalue": "1.593e-01"
- },
- {
- "index": 70,
- "trait_id": "1415752_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415752_at:HC_M2_0606_P:4db5c0fbe608b70cb257",
- "symbol": "C18orf32",
- "description": "putative NF-kappa-B-activating protein 200, C18orf32; 3' UTR",
- "location": "Chr18: 75.169011",
- "mean": "12.815",
- "additive": "0.093",
- "lod_score": "5.3",
- "lrs_location": "Chr18: 75.843607",
- "sample_r": "-0.048",
- "num_overlap": 67,
- "sample_p": "6.997e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.378",
- "tissue_pvalue": "5.664e-02"
- },
- {
- "index": 71,
- "trait_id": "1415749_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415749_a_at:HC_M2_0606_P:7d00997b6e9b339f534d",
- "symbol": "Rragc",
- "description": "Ras-related GTP binding C; mid-distal 3' UTR",
- "location": "Chr4: 123.613693",
- "mean": "11.140",
- "additive": "-0.057",
- "lod_score": "2.2",
- "lrs_location": "Chr12: 76.396441",
- "sample_r": "-0.044",
- "num_overlap": 67,
- "sample_p": "7.244e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.158",
- "tissue_pvalue": "4.411e-01"
- },
- {
- "index": 72,
- "trait_id": "1415673_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415673_at:HC_M2_0606_P:6eb18e73a45c97c7f8d0",
- "symbol": "Psph",
- "description": "phosphoserine phosphatase; last three exons and distal 3' UTR",
- "location": "Chr5: 130.271465",
- "mean": "9.690",
- "additive": "-0.121",
- "lod_score": "6.9",
- "lrs_location": "Chr1: 174.792334",
- "sample_r": "-0.043",
- "num_overlap": 67,
- "sample_p": "7.325e-01",
- "lit_corr": "--",
- "tissue_corr": "0.070",
- "tissue_pvalue": "7.354e-01"
- },
- {
- "index": 73,
- "trait_id": "1415718_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415718_at:HC_M2_0606_P:9714b7b3046b5c8bf4a0",
- "symbol": "Sap30l",
- "description": "SAP30-like (histone deacetylase complex subunit, sin3A-associated protein p30-like protein); last three exons and 3' UTR",
- "location": "Chr11: 57.619548",
- "mean": "10.407",
- "additive": "0.170",
- "lod_score": "12.8",
- "lrs_location": "Chr11: 57.088037",
- "sample_r": "0.041",
- "num_overlap": 67,
- "sample_p": "7.418e-01",
- "lit_corr": "--",
- "tissue_corr": "0.016",
- "tissue_pvalue": "9.370e-01"
- },
- {
- "index": 74,
- "trait_id": "1415755_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415755_a_at:HC_M2_0606_P:e23340ac6458755b9d1e",
- "symbol": "Ube2v1",
- "description": "ubiquitin-conjugating enzyme E2 variant 1",
- "location": "Chr2: 23.477654",
- "mean": "12.282",
- "additive": "0.053",
- "lod_score": "2.2",
- "lrs_location": "Chr6: 127.954548",
- "sample_r": "0.040",
- "num_overlap": 67,
- "sample_p": "7.490e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.321",
- "tissue_pvalue": "1.102e-01"
- },
- {
- "index": 75,
- "trait_id": "1415694_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415694_at:HC_M2_0606_P:38c96bb74d8916f0c519",
- "symbol": "Wars",
- "description": "tryptophanyl-tRNA synthetase; alternative 3' UTR (short form, test Mendelian 12.109, BXD hippocampus, B high)",
- "location": "Chr12: 110.098698",
- "mean": "8.523",
- "additive": "-0.938",
- "lod_score": "32.3",
- "lrs_location": "Chr12: 110.136559",
- "sample_r": "-0.039",
- "num_overlap": 67,
- "sample_p": "7.559e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.275",
- "tissue_pvalue": "1.738e-01"
- },
- {
- "index": 76,
- "trait_id": "1415744_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415744_at:HC_M2_0606_P:38f9abcb635f29e5871c",
- "symbol": "Pfdn6",
- "description": "prefoldin subunit 6 (H2-K region expressed gene 2); 5' UTR, exons 1, 3, 4, and 3' UTR",
- "location": "Chr17: 34.075883",
- "mean": "11.324",
- "additive": "-0.157",
- "lod_score": "11.0",
- "lrs_location": "Chr17: 33.247164",
- "sample_r": "0.038",
- "num_overlap": 67,
- "sample_p": "7.626e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 77,
- "trait_id": "1415700_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415700_a_at:HC_M2_0606_P:95582b9daa0776067713",
- "symbol": "Ssr3",
- "description": "signal sequence receptor, gamma (translocon-associated protein gamma); mid-distal 3' UTR",
- "location": "Chr3: 65.183917",
- "mean": "12.068",
- "additive": "0.067",
- "lod_score": "2.1",
- "lrs_location": "Chr7: 27.852865",
- "sample_r": "0.036",
- "num_overlap": 67,
- "sample_p": "7.742e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.354",
- "tissue_pvalue": "7.623e-02"
- },
- {
- "index": 78,
- "trait_id": "1415687_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415687_a_at:HC_M2_0606_P:f15bcfef7839d22ca5a3",
- "symbol": "Psap",
- "description": "prosaposin; mid and distal 3' UTR",
- "location": "Chr10: 59.764772",
- "mean": "14.976",
- "additive": "0.121",
- "lod_score": "2.0",
- "lrs_location": "Chr5: 4.468199",
- "sample_r": "0.035",
- "num_overlap": 67,
- "sample_p": "7.777e-01",
- "lit_corr": "--",
- "tissue_corr": "0.078",
- "tissue_pvalue": "7.058e-01"
- },
- {
- "index": 79,
- "trait_id": "1415729_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415729_at:HC_M2_0606_P:08dc70633663e17111dd",
- "symbol": "Pdpk1",
- "description": "3-phosphoinositide dependent protein kinase-1; distal 3' UTR",
- "location": "Chr17: 24.210667",
- "mean": "12.376",
- "additive": "-0.081",
- "lod_score": "3.0",
- "lrs_location": "Chr2: 55.266330",
- "sample_r": "-0.029",
- "num_overlap": 67,
- "sample_p": "8.147e-01",
- "lit_corr": "--",
- "tissue_corr": "0.290",
- "tissue_pvalue": "1.506e-01"
- },
- {
- "index": 80,
- "trait_id": "1415672_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415672_at:HC_M2_0606_P:d6a7286d4957f3487196",
- "symbol": "Golga7",
- "description": "golgi autoantigen, golgin subfamily a, 7",
- "location": "Chr8: 24.351869",
- "mean": "13.218",
- "additive": "0.063",
- "lod_score": "2.6",
- "lrs_location": "Chr13: 120.059030",
- "sample_r": "-0.027",
- "num_overlap": 67,
- "sample_p": "8.305e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.456",
- "tissue_pvalue": "1.919e-02"
- },
- {
- "index": 81,
- "trait_id": "1415713_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415713_a_at:HC_M2_0606_P:e22be15fd9ade623e3bb",
- "symbol": "Ddx24",
- "description": "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24; last two exons",
- "location": "Chr12: 104.646500",
- "mean": "11.808",
- "additive": "0.052",
- "lod_score": "3.1",
- "lrs_location": "Chr9: 15.693672",
- "sample_r": "-0.026",
- "num_overlap": 67,
- "sample_p": "8.322e-01",
- "lit_corr": "--",
- "tissue_corr": "0.338",
- "tissue_pvalue": "9.077e-02"
- },
- {
- "index": 82,
- "trait_id": "1415683_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415683_at:HC_M2_0606_P:f544e88da2dd8adb0b3f",
- "symbol": "Nmt1",
- "description": "N-myristoyltransferase 1; exons 10 and 11, and 3' UTR",
- "location": "Chr11: 102.926047",
- "mean": "12.261",
- "additive": "-0.070",
- "lod_score": "2.6",
- "lrs_location": "Chr6: 101.797292",
- "sample_r": "0.026",
- "num_overlap": 67,
- "sample_p": "8.375e-01",
- "lit_corr": "--",
- "tissue_corr": "0.366",
- "tissue_pvalue": "6.559e-02"
- },
- {
- "index": 83,
- "trait_id": "1415701_x_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415701_x_at:HC_M2_0606_P:8faa1e92ec8fc8cf33b5",
- "symbol": "Rpl23",
- "description": "ribosomal protein L23; spans exons 1, 2, 3, 4, and intron 4, and proximal 3' UTR",
- "location": "Chr11: 97.639386",
- "mean": "16.236",
- "additive": "0.067",
- "lod_score": "2.7",
- "lrs_location": "Chr2: 162.502590",
- "sample_r": "0.024",
- "num_overlap": 67,
- "sample_p": "8.474e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.036",
- "tissue_pvalue": "8.630e-01"
- },
- {
- "index": 84,
- "trait_id": "1415681_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415681_at:HC_M2_0606_P:96ceed972f5f3da9d52d",
- "symbol": "Mrpl43",
- "description": "mitochondrial ribosomal protein L43",
- "location": "Chr19: 45.079983",
- "mean": "10.604",
- "additive": "-0.058",
- "lod_score": "2.1",
- "lrs_location": "Chr7: 90.186486",
- "sample_r": "-0.021",
- "num_overlap": 67,
- "sample_p": "8.669e-01",
- "lit_corr": "--",
- "tissue_corr": "0.362",
- "tissue_pvalue": "6.958e-02"
- },
- {
- "index": 85,
- "trait_id": "1415691_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415691_at:HC_M2_0606_P:c6a3213115c205f73f86",
- "symbol": "Dlg1",
- "description": "discs, large homolog 1 (presynaptic protein SAP97); distal 3' UTR",
- "location": "Chr16: 31.872849",
- "mean": "11.782",
- "additive": "0.088",
- "lod_score": "2.9",
- "lrs_location": "Chr17: 55.490261",
- "sample_r": "-0.020",
- "num_overlap": 67,
- "sample_p": "8.731e-01",
- "lit_corr": "--",
- "tissue_corr": "0.015",
- "tissue_pvalue": "9.426e-01"
- },
- {
- "index": 86,
- "trait_id": "1415715_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415715_at:HC_M2_0606_P:8c7d719635beb0f7a9f5",
- "symbol": "Slbp",
- "description": "stem-loop binding protein",
- "location": "Chr5: 33.995959",
- "mean": "9.003",
- "additive": "0.051",
- "lod_score": "2.2",
- "lrs_location": "Chr11: 69.415410",
- "sample_r": "-0.020",
- "num_overlap": 67,
- "sample_p": "8.749e-01",
- "lit_corr": "--",
- "tissue_corr": "0.090",
- "tissue_pvalue": "6.621e-01"
- },
- {
- "index": 87,
- "trait_id": "1415751_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415751_at:HC_M2_0606_P:d0d8a9fa8a2b142d4374",
- "symbol": "Hb1bp3",
- "description": "heterochromatin protein 1-binding protein 3",
- "location": "Chr4: 137.798500",
- "mean": "12.239",
- "additive": "-0.168",
- "lod_score": "14.7",
- "lrs_location": "Chr4: 138.152371",
- "sample_r": "0.019",
- "num_overlap": 67,
- "sample_p": "8.773e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 88,
- "trait_id": "1415764_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415764_at:HC_M2_0606_P:8a23b78d5d55a0026ceb",
- "symbol": "Cpsf7",
- "description": "cleavage and polyadenylation specificity factor 7",
- "location": "Chr1: 135.516541",
- "mean": "11.499",
- "additive": "-0.352",
- "lod_score": "28.8",
- "lrs_location": "Chr1: 135.115363",
- "sample_r": "-0.019",
- "num_overlap": 67,
- "sample_p": "8.787e-01",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 89,
- "trait_id": "1415724_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415724_a_at:HC_M2_0606_P:4ff4b2d244043dc3b03e",
- "symbol": "Cdc42",
- "description": "cell division cycle 42 (activator of Rac); mid-distal 3' UTR",
- "location": "Chr4: 136.876012",
- "mean": "11.795",
- "additive": "-0.120",
- "lod_score": "5.5",
- "lrs_location": "Chr1: 172.981863",
- "sample_r": "0.019",
- "num_overlap": 67,
- "sample_p": "8.792e-01",
- "lit_corr": "--",
- "tissue_corr": "0.073",
- "tissue_pvalue": "7.233e-01"
- },
- {
- "index": 90,
- "trait_id": "1415737_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415737_at:HC_M2_0606_P:c667a35a9b2b78172117",
- "symbol": "Rfk",
- "description": "riboflavin kinase; distal 3' UTR",
- "location": "Chr19: 17.475267",
- "mean": "11.552",
- "additive": "0.414",
- "lod_score": "35.4",
- "lrs_location": "Chr19: 16.955950",
- "sample_r": "0.019",
- "num_overlap": 67,
- "sample_p": "8.810e-01",
- "lit_corr": "--",
- "tissue_corr": "0.117",
- "tissue_pvalue": "5.681e-01"
- },
- {
- "index": 91,
- "trait_id": "1415738_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415738_at:HC_M2_0606_P:304349c531fb99926720",
- "symbol": "Txndc12",
- "description": "thioredoxin domain-containing protein 12; 3' UTR",
- "location": "Chr4: 108.534146",
- "mean": "9.375",
- "additive": "-0.103",
- "lod_score": "3.2",
- "lrs_location": "Chr1: 172.981863",
- "sample_r": "-0.016",
- "num_overlap": 67,
- "sample_p": "9.004e-01",
- "lit_corr": "--",
- "tissue_corr": "0.135",
- "tissue_pvalue": "5.114e-01"
- },
- {
- "index": 92,
- "trait_id": "1415735_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415735_at:HC_M2_0606_P:f30f5a5f571c8c61d459",
- "symbol": "Ddb1",
- "description": "damage-specific DNA binding protein 1, 127 kDa",
- "location": "Chr19: 10.703737",
- "mean": "10.647",
- "additive": "-0.085",
- "lod_score": "5.1",
- "lrs_location": "Chr16: 28.990480",
- "sample_r": "0.016",
- "num_overlap": 67,
- "sample_p": "9.008e-01",
- "lit_corr": "--",
- "tissue_corr": "0.248",
- "tissue_pvalue": "2.217e-01"
- },
- {
- "index": 93,
- "trait_id": "1415684_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415684_at:HC_M2_0606_P:710753b49f7e38406e4b",
- "symbol": "Atg5",
- "description": "autophagy related 5; mid 3' UTR",
- "location": "Chr10: 44.083511",
- "mean": "8.854",
- "additive": "-0.068",
- "lod_score": "2.2",
- "lrs_location": "Chr6: 145.406059",
- "sample_r": "-0.014",
- "num_overlap": 67,
- "sample_p": "9.086e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.109",
- "tissue_pvalue": "5.954e-01"
- },
- {
- "index": 94,
- "trait_id": "1415686_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415686_at:HC_M2_0606_P:455a84fffcd7a0997580",
- "symbol": "Rab14",
- "description": "Rab GTPase family member 14",
- "location": "Chr2: 35.036216",
- "mean": "12.112",
- "additive": "0.110",
- "lod_score": "3.6",
- "lrs_location": "Chr14: 124.508018",
- "sample_r": "-0.013",
- "num_overlap": 67,
- "sample_p": "9.139e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.056",
- "tissue_pvalue": "7.850e-01"
- },
- {
- "index": 95,
- "trait_id": "1415685_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415685_at:HC_M2_0606_P:60c84786fe2f4a62d13d",
- "symbol": "Mtif2",
- "description": "mitochondrial translational initiation factor 2",
- "location": "Chr11: 29.442428",
- "mean": "9.271",
- "additive": "-0.367",
- "lod_score": "23.1",
- "lrs_location": "Chr11: 28.975002",
- "sample_r": "0.012",
- "num_overlap": 67,
- "sample_p": "9.259e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.358",
- "tissue_pvalue": "7.272e-02"
- },
- {
- "index": 96,
- "trait_id": "1415679_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415679_at:HC_M2_0606_P:513339a6b22faab7d8f6",
- "symbol": "Psenen",
- "description": "presenilin enhancer 2; 5' UTR, all exons, and 3' UTR",
- "location": "Chr7: 31.346914",
- "mean": "11.480",
- "additive": "-0.283",
- "lod_score": "19.1",
- "lrs_location": "Chr7: 31.505577",
- "sample_r": "-0.011",
- "num_overlap": 67,
- "sample_p": "9.286e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.002",
- "tissue_pvalue": "9.929e-01"
- },
- {
- "index": 97,
- "trait_id": "1415710_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415710_at:HC_M2_0606_P:4b8e32a96cf0e9bb30d3",
- "symbol": "Cox18",
- "description": "cytochrome c oxidase assembly protein 18; last three exons and proximal 3' UTR",
- "location": "Chr5: 90.644087",
- "mean": "9.513",
- "additive": "0.402",
- "lod_score": "33.4",
- "lrs_location": "Chr5: 90.500265",
- "sample_r": "0.010",
- "num_overlap": 67,
- "sample_p": "9.360e-01",
- "lit_corr": "--",
- "tissue_corr": "0.420",
- "tissue_pvalue": "3.257e-02"
- },
- {
- "index": 98,
- "trait_id": "1415702_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415702_a_at:HC_M2_0606_P:7ef725f27498e294d14a",
- "symbol": "Ctbp1",
- "description": "C-terminal binding protein 1; 3' UTR",
- "location": "Chr5: 33.590456",
- "mean": "12.530",
- "additive": "-0.056",
- "lod_score": "2.3",
- "lrs_location": "Chr12: 76.993653",
- "sample_r": "-0.010",
- "num_overlap": 67,
- "sample_p": "9.372e-01",
- "lit_corr": "--",
- "tissue_corr": "0.514",
- "tissue_pvalue": "7.288e-03"
- },
- {
- "index": 99,
- "trait_id": "1415711_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415711_at:HC_M2_0606_P:f71bb40cdefd07ae95d6",
- "symbol": "Arfgef1",
- "description": "ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited); 3' UTR",
- "location": "Chr18: 22.122655",
- "mean": "11.617",
- "additive": "-0.055",
- "lod_score": "3.3",
- "lrs_location": "Chr2: 50.500580",
- "sample_r": "-0.003",
- "num_overlap": 67,
- "sample_p": "9.802e-01",
- "lit_corr": "--",
- "tissue_corr": "-0.020",
- "tissue_pvalue": "9.216e-01"
- },
- {
- "index": 100,
- "trait_id": "1415726_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1415726_at:HC_M2_0606_P:89e8ab5b988a202a2fb0",
- "symbol": "Ankrd17",
- "description": "ankyrin repeat domain protein 17; last exon and proximal 3' UTR",
- "location": "Chr5: 90.657781",
- "mean": "11.533",
- "additive": "0.046",
- "lod_score": "2.0",
- "lrs_location": "Chr14: 42.819085",
- "sample_r": "0.000",
- "num_overlap": 67,
- "sample_p": "9.991e-01",
- "lit_corr": "--",
- "tissue_corr": "0.530",
- "tissue_pvalue": "5.382e-03"
- }
-] \ No newline at end of file
diff --git a/tests/unit/correlation/group_data_test.json b/tests/unit/correlation/group_data_test.json
deleted file mode 100644
index 9a73a46..0000000
--- a/tests/unit/correlation/group_data_test.json
+++ /dev/null
@@ -1,214 +0,0 @@
-{
- "name":"BXD",
- "id":1,
- "genetic_type":"riset",
- "f1list":"None",
- "parlist":"None",
- "mapping_id":"1",
- "mapping_names":[
- "GEMMA",
- "QTLReaper",
- "R/qtl"
- ],
- "species":"mouse",
- "samplelist":[
- "BXD1",
- "BXD2",
- "BXD5",
- "BXD6",
- "BXD8",
- "BXD9",
- "BXD11",
- "BXD12",
- "BXD13",
- "BXD14",
- "BXD15",
- "BXD16",
- "BXD18",
- "BXD19",
- "BXD20",
- "BXD21",
- "BXD22",
- "BXD23",
- "BXD24",
- "BXD24a",
- "BXD25",
- "BXD27",
- "BXD28",
- "BXD29",
- "BXD30",
- "BXD31",
- "BXD32",
- "BXD33",
- "BXD34",
- "BXD35",
- "BXD36",
- "BXD37",
- "BXD38",
- "BXD39",
- "BXD40",
- "BXD41",
- "BXD42",
- "BXD43",
- "BXD44",
- "BXD45",
- "BXD48",
- "BXD48a",
- "BXD49",
- "BXD50",
- "BXD51",
- "BXD52",
- "BXD53",
- "BXD54",
- "BXD55",
- "BXD56",
- "BXD59",
- "BXD60",
- "BXD61",
- "BXD62",
- "BXD63",
- "BXD64",
- "BXD65",
- "BXD65a",
- "BXD65b",
- "BXD66",
- "BXD67",
- "BXD68",
- "BXD69",
- "BXD70",
- "BXD71",
- "BXD72",
- "BXD73",
- "BXD73a",
- "BXD73b",
- "BXD74",
- "BXD75",
- "BXD76",
- "BXD77",
- "BXD78",
- "BXD79",
- "BXD81",
- "BXD83",
- "BXD84",
- "BXD85",
- "BXD86",
- "BXD87",
- "BXD88",
- "BXD89",
- "BXD90",
- "BXD91",
- "BXD93",
- "BXD94",
- "BXD95",
- "BXD98",
- "BXD99",
- "BXD100",
- "BXD101",
- "BXD102",
- "BXD104",
- "BXD105",
- "BXD106",
- "BXD107",
- "BXD108",
- "BXD109",
- "BXD110",
- "BXD111",
- "BXD112",
- "BXD113",
- "BXD114",
- "BXD115",
- "BXD116",
- "BXD117",
- "BXD119",
- "BXD120",
- "BXD121",
- "BXD122",
- "BXD123",
- "BXD124",
- "BXD125",
- "BXD126",
- "BXD127",
- "BXD128",
- "BXD128a",
- "BXD130",
- "BXD131",
- "BXD132",
- "BXD133",
- "BXD134",
- "BXD135",
- "BXD136",
- "BXD137",
- "BXD138",
- "BXD139",
- "BXD141",
- "BXD142",
- "BXD144",
- "BXD145",
- "BXD146",
- "BXD147",
- "BXD148",
- "BXD149",
- "BXD150",
- "BXD151",
- "BXD152",
- "BXD153",
- "BXD154",
- "BXD155",
- "BXD156",
- "BXD157",
- "BXD160",
- "BXD161",
- "BXD162",
- "BXD165",
- "BXD168",
- "BXD169",
- "BXD170",
- "BXD171",
- "BXD172",
- "BXD173",
- "BXD174",
- "BXD175",
- "BXD176",
- "BXD177",
- "BXD178",
- "BXD180",
- "BXD181",
- "BXD183",
- "BXD184",
- "BXD186",
- "BXD187",
- "BXD188",
- "BXD189",
- "BXD190",
- "BXD191",
- "BXD192",
- "BXD193",
- "BXD194",
- "BXD195",
- "BXD196",
- "BXD197",
- "BXD198",
- "BXD199",
- "BXD200",
- "BXD201",
- "BXD202",
- "BXD203",
- "BXD204",
- "BXD205",
- "BXD206",
- "BXD207",
- "BXD208",
- "BXD209",
- "BXD210",
- "BXD211",
- "BXD212",
- "BXD213",
- "BXD214",
- "BXD215",
- "BXD216",
- "BXD217",
- "BXD218",
- "BXD219",
- "BXD220"
- ]
-} \ No newline at end of file
diff --git a/tests/unit/correlation/my_results.json b/tests/unit/correlation/my_results.json
deleted file mode 100644
index 2061c6e..0000000
--- a/tests/unit/correlation/my_results.json
+++ /dev/null
@@ -1,388 +0,0 @@
-[
-
- {
- "sample_r_correlation_using_genenetwork3":"Results",
-
- },
-
- {
- "index": 1,
- "trait_id": "1445813_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1445813_at:HC_M2_0606_P:ca1b85915ccba7198af3",
- "symbol": "0610012K18Rik",
- "description": "RIKEN cDNA 0610012H03 (no human homolog defined)",
- "location": "Chr17: 14.966404",
- "mean": "6.643",
- "additive": "0.042",
- "lod_score": "2.6",
- "lrs_location": "Chr5: 133.538653",
- "sample_r": "-0.694",
- "num_overlap": 67,
- "sample_p": "7.244e-11",
- "lit_corr": "--",
- "tissue_corr": "--",
- "tissue_pvalue": "--"
- },
- {
- "index": 2,
- "trait_id": "1439910_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1439910_a_at:HC_M2_0606_P:0c4c7a3cb088699af36c",
- "symbol": "Tradd",
- "description": "TNFRSF1A-associated via death domain",
- "location": "Chr8: 107.783836",
- "mean": "7.449",
- "additive": "0.039",
- "lod_score": "1.7",
- "lrs_location": "Chr1: 195.987783",
- "sample_r": "-0.692",
- "num_overlap": 67,
- "sample_p": "9.012e-11",
- "lit_corr": "--",
- "tissue_corr": "-0.285",
- "tissue_pvalue": "1.575e-01"
- },
- {
- "index": 3,
- "trait_id": "1421499_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1421499_a_at:HC_M2_0606_P:b807253e0829c2592ceb",
- "symbol": "Ptpn14",
- "description": "protein tyrosine phosphatase, non-receptor type 14",
- "location": "Chr1: 191.689356",
- "mean": "6.655",
- "additive": "0.049",
- "lod_score": "2.4",
- "lrs_location": "Chr1: 197.014645",
- "sample_r": "-0.691",
- "num_overlap": 67,
- "sample_p": "1.009e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.242",
- "tissue_pvalue": "2.337e-01"
- },
- {
- "index": 4,
- "trait_id": "1421167_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1421167_at:HC_M2_0606_P:d7b29d02c306e1ae105a",
- "symbol": "Atp11a",
- "description": "ATPase, class VI, type 11A; last four exons and 3' UTR",
- "location": "Chr8: 12.856932",
- "mean": "7.341",
- "additive": "0.050",
- "lod_score": "1.7",
- "lrs_location": "Chr9: 62.226499",
- "sample_r": "-0.690",
- "num_overlap": 67,
- "sample_p": "1.059e-10",
- "lit_corr": "--",
- "tissue_corr": "0.154",
- "tissue_pvalue": "4.522e-01"
- },
- {
- "index": 5,
- "trait_id": "1436525_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1436525_at:HC_M2_0606_P:b36b6c4053c40cc5b25b",
- "symbol": "Ap3s2",
- "description": "adaptor-related protein complex 3, sigma 2 subunit",
- "location": "Chr7: 87.022674",
- "mean": "8.227",
- "additive": "-0.070",
- "lod_score": "3.0",
- "lrs_location": "Chr4: 63.346622",
- "sample_r": "-0.679",
- "num_overlap": 67,
- "sample_p": "2.627e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.059",
- "tissue_pvalue": "7.750e-01"
- },
- {
- "index": 6,
- "trait_id": "1450824_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1450824_at:HC_M2_0606_P:fa9b15d1d4a2d629decb",
- "symbol": "Ptch1",
- "description": "patched homolog 1",
- "location": "Chr13: 63.612887",
- "mean": "7.105",
- "additive": "0.070",
- "lod_score": "3.9",
- "lrs_location": "Chr5: 133.538653",
- "sample_r": "-0.679",
- "num_overlap": 67,
- "sample_p": "2.771e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.360",
- "tissue_pvalue": "7.075e-02"
- },
- {
- "index": 7,
- "trait_id": "1450540_x_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1450540_x_at:HC_M2_0606_P:0836630187705e0a98ed",
- "symbol": "Krtap5-1",
- "description": "keratin associated protein 5-1",
- "location": "Chr7: 149.482282",
- "mean": "7.584",
- "additive": "0.059",
- "lod_score": "2.2",
- "lrs_location": "Chr5: 140.893042",
- "sample_r": "-0.678",
- "num_overlap": 67,
- "sample_p": "2.828e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.486",
- "tissue_pvalue": "1.174e-02"
- },
- {
- "index": 8,
- "trait_id": "1454403_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1454403_at:HC_M2_0606_P:d6625a44bb78d0c9a7bc",
- "symbol": "Fgd5",
- "description": "FYVE, RhoGEF and PH domain containing 5",
- "location": "Chr6: 91.964079",
- "mean": "6.447",
- "additive": "-0.036",
- "lod_score": "1.8",
- "lrs_location": "Chr8: 7.701081",
- "sample_r": "-0.669",
- "num_overlap": 67,
- "sample_p": "5.895e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.209",
- "tissue_pvalue": "3.062e-01"
- },
- {
- "index": 9,
- "trait_id": "1444162_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1444162_at:HC_M2_0606_P:fea27946a4ed1ee2b47a",
- "symbol": "Frs2",
- "description": "fibroblast growth factor receptor substrate 2",
- "location": "Chr10: 116.521472",
- "mean": "5.677",
- "additive": "-0.040",
- "lod_score": "1.8",
- "lrs_location": "Chr4: 66.843058",
- "sample_r": "-0.666",
- "num_overlap": 67,
- "sample_p": "7.946e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.241",
- "tissue_pvalue": "2.352e-01"
- },
- {
- "index": 10,
- "trait_id": "1451876_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1451876_a_at:HC_M2_0606_P:eb879785591c3c2addeb",
- "symbol": "Trp63",
- "description": "transformation related protein 63",
- "location": "Chr16: 25.884897",
- "mean": "6.207",
- "additive": "0.059",
- "lod_score": "2.0",
- "lrs_location": "Chr9: 74.382952",
- "sample_r": "-0.664",
- "num_overlap": 67,
- "sample_p": "8.743e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.187",
- "tissue_pvalue": "3.601e-01"
- },
- {
- "index": 11,
- "trait_id": "1457795_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1457795_at:HC_M2_0606_P:617d62e702f1f04b065d",
- "symbol": "Scamp4",
- "description": "secretory carrier membrane protein 4",
- "location": "Chr10: 80.076487",
- "mean": "7.060",
- "additive": "-0.042",
- "lod_score": "2.4",
- "lrs_location": "Chr11: 58.923978",
- "sample_r": "-0.663",
- "num_overlap": 67,
- "sample_p": "9.806e-10",
- "lit_corr": "--",
- "tissue_corr": "-0.040",
- "tissue_pvalue": "8.462e-01"
- },
- {
- "index": 12,
- "trait_id": "1439472_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1439472_at:HC_M2_0606_P:f52f356bf5d00add1ba9",
- "symbol": "Gcn1l1",
- "description": "general control of amino-acid synthesis 1-like 1",
- "location": "Chr5: 116.033483",
- "mean": "7.325",
- "additive": "0.058",
- "lod_score": "3.1",
- "lrs_location": "Chr1: 196.404284",
- "sample_r": "-0.662",
- "num_overlap": 67,
- "sample_p": "1.075e-09",
- "lit_corr": "--",
- "tissue_corr": "-0.205",
- "tissue_pvalue": "3.157e-01"
- },
- {
- "index": 13,
- "trait_id": "1422074_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1422074_at:HC_M2_0606_P:4acd73cfd3d194327d79",
- "symbol": "Cdx2",
- "description": "caudal type homeo box 2",
- "location": "Chr5: 148.113293",
- "mean": "6.415",
- "additive": "-0.037",
- "lod_score": "1.8",
- "lrs_location": "Chr2: 180.825581",
- "sample_r": "-0.661",
- "num_overlap": 67,
- "sample_p": "1.140e-09",
- "lit_corr": "--",
- "tissue_corr": "0.002",
- "tissue_pvalue": "9.926e-01"
- },
- {
- "index": 14,
- "trait_id": "1429140_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1429140_at:HC_M2_0606_P:16116d150fd7a8d09687",
- "symbol": "Spns3",
- "description": "spinster homolog 3; exons 10, 12, and proximal 3' UTR",
- "location": "Chr11: 72.311676",
- "mean": "7.194",
- "additive": "0.050",
- "lod_score": "2.1",
- "lrs_location": "Chr9: 69.810185",
- "sample_r": "-0.661",
- "num_overlap": 67,
- "sample_p": "1.175e-09",
- "lit_corr": "--",
- "tissue_corr": "0.557",
- "tissue_pvalue": "3.116e-03"
- },
- {
- "index": 15,
- "trait_id": "1437477_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1437477_at:HC_M2_0606_P:990d16df933d7bb03428",
- "symbol": "Lrrfip1",
- "description": "leucine rich repeat (in FLII) interacting protein 1",
- "location": "Chr1: 93.011523",
- "mean": "7.597",
- "additive": "0.068",
- "lod_score": "2.3",
- "lrs_location": "Chr5: 133.538653",
- "sample_r": "-0.658",
- "num_overlap": 67,
- "sample_p": "1.393e-09",
- "lit_corr": "--",
- "tissue_corr": "0.132",
- "tissue_pvalue": "5.204e-01"
- },
- {
- "index": 16,
- "trait_id": "1440212_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1440212_at:HC_M2_0606_P:01ae82e4856177dd9d89",
- "symbol": "Slc12a1",
- "description": "solute carrier family 12, member 1",
- "location": "Chr2: 124.990152",
- "mean": "7.061",
- "additive": "0.038",
- "lod_score": "2.2",
- "lrs_location": "Chr1: 193.731996",
- "sample_r": "-0.655",
- "num_overlap": 67,
- "sample_p": "1.769e-09",
- "lit_corr": "--",
- "tissue_corr": "0.028",
- "tissue_pvalue": "8.923e-01"
- },
- {
- "index": 17,
- "trait_id": "1419755_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1419755_at:HC_M2_0606_P:15fea7c69b0d5faa1298",
- "symbol": "Mfi2",
- "description": "antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5",
- "location": "Chr16: 31.898518",
- "mean": "6.697",
- "additive": "-0.038",
- "lod_score": "2.0",
- "lrs_location": "Chr4: 50.881071",
- "sample_r": "-0.654",
- "num_overlap": 67,
- "sample_p": "1.950e-09",
- "lit_corr": "--",
- "tissue_corr": "0.244",
- "tissue_pvalue": "2.305e-01"
- },
- {
- "index": 18,
- "trait_id": "1425457_a_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1425457_a_at:HC_M2_0606_P:669c485b158c0207026c",
- "symbol": "Grb10",
- "description": "growth factor receptor bound protein 10",
- "location": "Chr11: 11.833500",
- "mean": "6.515",
- "additive": "0.081",
- "lod_score": "3.9",
- "lrs_location": "Chr5: 133.538653",
- "sample_r": "-0.652",
- "num_overlap": 67,
- "sample_p": "2.295e-09",
- "lit_corr": "--",
- "tissue_corr": "-0.090",
- "tissue_pvalue": "6.617e-01"
- },
- {
- "index": 19,
- "trait_id": "1431329_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1431329_at:HC_M2_0606_P:a6df7ed818ea0042c550",
- "symbol": "Nphp4",
- "description": "nephronophthisis 4 (renal tubular development and function)",
- "location": "Chr4: 151.863271",
- "mean": "6.191",
- "additive": "0.039",
- "lod_score": "1.9",
- "lrs_location": "ChrX: 112.637353",
- "sample_r": "-0.652",
- "num_overlap": 67,
- "sample_p": "2.330e-09",
- "lit_corr": "--",
- "tissue_corr": "-0.104",
- "tissue_pvalue": "6.144e-01"
- },
- {
- "index": 20,
- "trait_id": "1443987_at",
- "dataset": "HC_M2_0606_P",
- "hmac": "1443987_at:HC_M2_0606_P:681e6c787b4d652d0c07",
- "symbol": "Klhl18",
- "description": "kelch-like 18 (Drosophila)",
- "location": "Chr9: 110.330597",
- "mean": "7.244",
- "additive": "-0.070",
- "lod_score": "2.1",
- "lrs_location": "Chr15: 13.149248",
- "sample_r": "-0.650",
- "num_overlap": 67,
- "sample_p": "2.561e-09",
- "lit_corr": "--",
- "tissue_corr": "-0.200",
- "tissue_pvalue": "3.270e-01"
- }
-] \ No newline at end of file
diff --git a/tests/unit/correlation/test_correlation_computations.py b/tests/unit/correlation/test_correlation_computations.py
deleted file mode 100644
index dbb2587..0000000
--- a/tests/unit/correlation/test_correlation_computations.py
+++ /dev/null
@@ -1,65 +0,0 @@
-"""module for testing correlation/correlation_computations"""
-
-import unittest
-from gn3.correlation.correlation_computations import compute_correlation
-
-
-# mock for calculating correlation function
-
-def mock_get_loading_page_data(initial_start_vars):
- """function to mock filtering input"""
- results = {'start_vars':
- {'genofile': 'SAMPLE:X', 'dataset': 'HC_M2_0606_P',
- 'sample_vals': '{"C57BL/6J":"7.197","DBA/2J":"7.148","B6D2F1":"6.999"}',
- 'primary_samples': 'C57BL/6J,DBA/2J,B6D2F1',
- 'n_samples': 3,
- 'wanted_inputs': "sample_vals,dataset,genofile,primary_samples"}}
-
- return results
-
-
-class MockCorrelationResults:
- """mock class for CorrelationResults"""
-
- def __init__(self, start_vars):
- for _key, value in start_vars.items():
- self.value = value
-
- self.assert_start_vars(start_vars)
-
- @staticmethod
- def assert_start_vars(start_vars):
- """assert data required is supplied"""
- assert "wanted_inputs" in start_vars
-
- def do_correlation(self, start_vars):
- """mock method for doing correlation"""
-
- return {
- "results": "success"
- }
-
-
-class TestCorrelationUtility(unittest.TestCase):
- """tests for correlation computations"""
-
- def test_compute_correlation(self):
- """test function for doing correlation"""
-
- sample_vals = """{"C57BL/6J":"7.197","DBA/2J":"7.148","B6D2F1":"6.999"}"""
-
- correlation_input_data = {
- "wanted_inputs": "sample_vals,dataset,genofile,primary_samples",
- "genofile": "SAMPLE:X",
- "dataset": "HC_M2_0606_P",
-
- "sample_vals": sample_vals,
- "primary_samples": "C57BL/6J,DBA/2J,B6D2F1"
-
- }
- correlation_results = compute_correlation(
- correlation_input_data=correlation_input_data,
- correlation_results=MockCorrelationResults)
- results = {"results": "success"}
-
- self.assertEqual(results,correlation_results)
diff --git a/tests/unit/correlation/test_show_corr_results.py b/tests/unit/correlation/test_show_corr_results.py
deleted file mode 100644
index 4846f5e..0000000
--- a/tests/unit/correlation/test_show_corr_results.py
+++ /dev/null
@@ -1,226 +0,0 @@
-"""module contains code for testing creating show correlation object"""
-
-import unittest
-import json
-import os
-from unittest import mock
-from types import SimpleNamespace
-from gn3.correlation.show_corr_results import CorrelationResults
-from gn3.correlation.show_corr_results import get_header_fields
-from gn3.correlation.show_corr_results import generate_corr_json
-# pylint: disable=unused-argument
-
-
-
-class ObjectMixin:
- """object for adding other methods"""
- def __str__(self):
- raise NotImplementedError
-
- def get_dict(self):
- raise NotImplementedError
-
-class MockGroup(ObjectMixin):
- """mock class for Group"""
-
- def __init__(self):
- self.samplelist = "add a mock for this"
- self.parlist = None
-
- self.filist = None
-
-class MockCreateTrait(ObjectMixin):
- """mock class for create trait"""
-
- def __init__(self):
- pass
-
- def get_dict(self):
- """class for getting dict items"""
- return self.__dict__
-
- def __str__(self):
- return self.__class__.__name__
-
-
-class MockCreateDataset:
- """mock class for create dataset"""
-
- def __init__(self):
-
- self.group = MockGroup()
-
- def get_trait_data(self, sample_keys):
- """method for getting trait data"""
- raise NotImplementedError()
-
- def retrieve_genes(self, symbol):
- """method for retrieving genes"""
- raise NotImplementedError()
-
-
-def file_path(relative_path):
- """getting abs path for file """
- # adopted from github
- dir_name = os.path.dirname(os.path.abspath(__file__))
- split_path = relative_path.split("/")
- new_path = os.path.join(dir_name, *split_path)
- return new_path
-
-
-def create_trait(dataset="Temp", name=None, cellid=None):
- """mock function for creating trait"""
- return "trait results"
-
-
-def create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=None):
- """mock function to create dataset """
- return "dataset results"
-
-
-def get_species(self, start_vars):
- """
- how this function works is that it sets the self.dataset and self.species and self.this_trait
- """
-
- with open(file_path("./dataset.json")) as dataset_file:
- results = json.load(dataset_file)
- self.dataset = SimpleNamespace(**results)
-
- with open(file_path("./group_data_test.json")) as group_file:
- results = json.load(group_file)
- self.group = SimpleNamespace(**results)
-
- self.dataset.group = self.group
-
- trait_dict = {'name': '1434568_at', 'dataset': self.dataset, 'cellid': None,
- 'identification': 'un-named trait', 'haveinfo': True, 'sequence': None}
-
- trait_obj = SimpleNamespace(**trait_dict)
-
- self.this_trait = trait_obj
-
- self.species = "this species data"
-
-
-class TestCorrelationResults(unittest.TestCase):
- """unittests for Correlation Results"""
-
- def setUp(self):
-
- with open(file_path("./correlation_test_data.json")) as json_file:
- self.correlation_data = json.load(json_file)
-
- def tearDown(self):
-
- self.correlation_data = ""
-
- def test_for_assertion(self):
- """test for assertion failures"""
- with self.assertRaises(AssertionError):
- _corr_results_object = CorrelationResults(start_vars={})
-
- @mock.patch("gn3.correlation.show_corr_results.CorrelationResults.process_samples")
- def test_do_correlation(self, process_samples):
- """test for doing correlation"""
- process_samples.return_value = None
- corr_object = CorrelationResults(start_vars=self.correlation_data)
-
- with self.assertRaises(Exception) as _error:
-
- # xtodo;to be completed
-
- _corr_results = corr_object.do_correlation(start_vars=self.correlation_data,
- create_dataset=create_dataset,
- create_trait=None,
- get_species_dataset_trait=get_species)
-
-
-
- def test_get_header_fields(self):
- expected = [
- ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Sample rho',
- 'N',
- 'Sample p(rho)',
- 'Lit rho',
- 'Tissue rho',
- 'Tissue p(rho)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect'],
-
- ['Index',
- 'ID',
- 'Location',
- 'Sample r',
- 'N',
- 'Sample p(r)']
-
- ]
- result1 = get_header_fields("ProbeSet", "spearman")
- result2 = get_header_fields("Other", "Other")
- self.assertEqual(result1, expected[0])
- self.assertEqual(result2, expected[1])
-
-
-
- @mock.patch("gn3.utility.hmac.data_hmac")
- def test_generate_corr_json(self, mock_data_hmac):
- mock_data_hmac.return_value = "hajsdiau"
-
- dataset = SimpleNamespace(**{"name": "the_name"})
- this_trait = SimpleNamespace(**{"name": "trait_test", "dataset": dataset})
- target_dataset = SimpleNamespace(**{"type": "Publish"})
- corr_trait_1 = SimpleNamespace(**{
- "name": "trait_1",
- "dataset": SimpleNamespace(**{"name": "dataset_1"}),
- "view": True,
- "abbreviation": "T1",
- "description_display": "Trait I description",
- "authors": "JM J,JYEW",
- "pubmed_id": "34n4nn31hn43",
- "pubmed_text": "2016",
- "pubmed_link": "https://www.load",
- "lod_score": "",
- "mean": "",
- "LRS_location_repr": "BXBS",
- "additive": "",
- "sample_r": 10.5,
- "num_overlap": 2,
- "sample_p": 5
-
-
-
-
- })
- corr_results = [corr_trait_1]
-
- dataset_type_other = {
- "location": "cx-3-4",
- "sample_4": 12.32,
- "num_overlap": 3,
- "sample_p": 10.34
- }
-
- expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
-
- results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
- dataset=dataset, target_dataset=target_dataset, for_api=True)
- self.assertEqual(expected_results, results1)
-
-
- def test_generate_corr_json_view_false(self):
- trait = SimpleNamespace(**{"view": False})
- corr_results = [trait]
- this_trait = SimpleNamespace(**{"name": "trait_test"})
- dataset = SimpleNamespace(**{"name": "the_name"})
-
- results_where_view_is_false = generate_corr_json(
- corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False)
- self.assertEqual(results_where_view_is_false, "[]") \ No newline at end of file
diff --git a/tests/unit/utility/__init__.py b/tests/unit/utility/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/tests/unit/utility/__init__.py
+++ /dev/null
diff --git a/tests/unit/utility/test_chunks.py b/tests/unit/utility/test_chunks.py
deleted file mode 100644
index 7c42b44..0000000
--- a/tests/unit/utility/test_chunks.py
+++ /dev/null
@@ -1,19 +0,0 @@
-"""Test chunking"""
-
-import unittest
-
-from gn3.utility.chunks import divide_into_chunks
-
-
-class TestChunks(unittest.TestCase):
- "Test Utility method for chunking"
- def test_divide_into_chunks(self):
- "Check that a list is chunked correctly"
- self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
- [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
- self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4),
- [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
- self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5),
- [[1, 2], [7, 3], [22, 8], [5, 22], [333]])
- self.assertEqual(divide_into_chunks([], 5),
- [[]])
diff --git a/tests/unit/utility/test_corr_result_helpers.py b/tests/unit/utility/test_corr_result_helpers.py
deleted file mode 100644
index ce5891f..0000000
--- a/tests/unit/utility/test_corr_result_helpers.py
+++ /dev/null
@@ -1,35 +0,0 @@
-""" Test correlation helper methods """
-
-import unittest
-from gn3.utility.corr_result_helpers import normalize_values
-from gn3.utility.corr_result_helpers import common_keys
-from gn3.utility.corr_result_helpers import normalize_values_with_samples
-
-
-class TestCorrelationHelpers(unittest.TestCase):
- """Test methods for normalising lists"""
-
- def test_normalize_values(self):
- """Test that a list is normalised correctly"""
- self.assertEqual(
- normalize_values([2.3, None, None, 3.2, 4.1, 5],\
- [3.4, 7.2, 1.3, None, 6.2, 4.1]),
- ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
- )
-
- def test_common_keys(self):
- """Test that common keys are returned as a list"""
- test_a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300)
- test_b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)
- self.assertEqual(sorted(common_keys(test_a, test_b)),
- ['BXD1', 'BXD14'])
-
- def test_normalize_values_with_samples(self):
- """Test that a sample(dict) is normalised correctly"""
- self.assertEqual(
- normalize_values_with_samples(
- dict(BXD1=9.113, BXD2=9.825, BXD14=8.985,
- BXD15=9.300, BXD20=9.300),
- dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)),
- (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2))
- )
diff --git a/tests/unit/utility/test_hmac.py b/tests/unit/utility/test_hmac.py
deleted file mode 100644
index eba25a3..0000000
--- a/tests/unit/utility/test_hmac.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""Test hmac utility functions"""
-# pylint: disable-all
-import unittest
-from unittest import mock
-
-from gn3.utility.hmac import data_hmac
-from gn3.utility.hmac import url_for_hmac
-from gn3.utility.hmac import hmac_creation
-
-
-class TestHmacUtil():
- """Test Utility method for hmac creation"""
-
- @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
- def test_hmac_creation(self):
- """Test hmac creation with a utf-8 string"""
- self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
-
- @mock.patch("utility.hmac.app.config",
- {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80'
- '\xd9\\H@\\\x9f`\x98d^'
- '\xb4a;\xc6OM\x946a\xbc'
- '\xfc\x80:*\xebc')})
- def test_hmac_creation_with_cookie(self):
- """Test hmac creation with a cookie"""
- cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce"
- uuid_, _, signature = cookie.partition(":")
- self.assertEqual(
- hmac_creation(uuid_),
- "af4fcf5eace9e7c864ce")
-
- @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
- def test_data_hmac(self):
- """Test data_hmac fn with a utf-8 string"""
- self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
-
- @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
- @mock.patch("utility.hmac.url_for")
- def test_url_for_hmac_with_plain_url(self, mock_url):
- """Test url_for_hmac without params"""
- mock_url.return_value = "https://mock_url.com/ファイ/"
- self.assertEqual(url_for_hmac("ファイ"),
- "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
-
- @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
- @mock.patch("utility.hmac.url_for")
- def test_url_for_hmac_with_param_in_url(self, mock_url):
- """Test url_for_hmac with params"""
- mock_url.return_value = "https://mock_url.com/?ファイ=1"
- self.assertEqual(url_for_hmac("ファイ"),
- "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:39:12 +0000