Added Amelie's rat data genotypes

Got human mapping mostly working

Fixed dataset dropdown menus

8 files changed, 136 insertions, 145 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index 9da6c4ea..d9bd6e41 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -245,6 +245,11 @@ To iterate through dictionary items: for X, Y in MyDictionary.items():
 
 ===========================================
 
+Change import path from command line
+export PYTHONPATH=~/gene/wqflask (or whatever)
+
+===========================================
+
 Create symbolic link:
 ln -s dir_to_link_to linking_dir
 
diff --git a/web/genotypes/HSNIH.geno.gz b/web/genotypes/HSNIH.geno.gz
new file mode 100755
index 00000000..96584768
--- /dev/null
+++ b/web/genotypes/HSNIH.geno.gz
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6648047c..a1e6b0d3 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -319,10 +319,9 @@ class GeneralTrait(object):
 
             #XZ: assign SQL query result to trait attributes.
             for i, field in enumerate(self.dataset.display_fields):
-                print("  mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
+                #print("  mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
                 holder = trait_info[i]
                 if isinstance(trait_info[i], basestring):
-                    print("is basestring")
                     holder = unicode(trait_info[i], "utf8")
                 setattr(self, field, holder)
 
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 716986db..d4511212 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -53,8 +53,8 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later
 SECUREDIR = GNROOT + 'secure/'
 COMMON_LIB = GNROOT + 'support/admin'
 HTMLPATH = GNROOT + 'web/'
-PYLMM_PATH = '/home/zas1024/'
-SNP_PATH = '/mnt/xvdf1/snps/' 
+PYLMM_PATH = '/home/zas1024/plink/'
+SNP_PATH = '/home/zas1024/snps/' 
 IMGDIR = HTMLPATH +'image/'
 IMAGESPATH = HTMLPATH + 'images/'
 UPLOADPATH = IMAGESPATH + 'upload/'
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d653fd2d..8cb94f20 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -47,6 +47,15 @@ import urlparse
 
 from pprint import pformat as pf
 
+#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI)
+
+# build MySql database connection
+
+#conn = Engine.connect()
+
+
+
+
 
 def parse_db_uri(db_uri):
     """Converts a database URI to the db name, host name, user name, and password"""
@@ -106,7 +115,7 @@ def build_types(species, group):
     (all types except phenotype/genotype are tissues)
      
     """
-    Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
+    Cursor.execute("""select distinct Tissue.Name, Tissue.Name
                        from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
                        where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
                        InbredSet.Name = %s and
@@ -161,13 +170,9 @@ def build_datasets(species, group, type_name):
 
 def main():
     """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
-<<<<<<< HEAD
 
     parse_db_uri(our_settings.DB_URI)
 
-=======
-    
->>>>>>> 1a3a456eb7635337a966913f2e2e75c8a89bb92e
     species = get_species()
     groups = get_groups(species)
     types = get_types(groups)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 422fa8af..07d70897 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -140,8 +140,6 @@ class CorrelationResults(object):
                 this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
                     this_trait_vals, target_vals)
 
-                print("num_overlap:", num_overlap)
-
                 if self.corr_method == 'pearson':
                     sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
                 else:
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 5bfc3a01..38a49f12 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -138,8 +138,8 @@ def run_human(pheno_vector,
         #print("***** Added to {} queue *****".format(key))
         for snp, this_id in plink_input:
             #with Bench("part before association"):
-            if count > 2000:
-                break
+            #if count > 2000:
+            #    break
             count += 1
 
             percent_complete = (float(count) / total_snps) * 100
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index a4de53bd..49c44fbd 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -798,10 +798,6 @@
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
                ],
                [
-                  "SA_M2_0905_R",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
-               ],
-               [
                   "SA_M2_0905_M",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
                ],
@@ -1052,10 +1048,6 @@
             ],
             "Cerebellum mRNA": [
                [
-                  "CB_M_1004_M",
-                  "SJUT Cerebellum mRNA M430 (Oct04) MAS5"
-               ],
-               [
                   "CB_M_1004_R",
                   "SJUT Cerebellum mRNA M430 (Oct04) RMA"
                ],
@@ -1064,6 +1056,10 @@
                   "SJUT Cerebellum mRNA M430 (Oct04) PDNN"
                ],
                [
+                  "CB_M_1004_M",
+                  "SJUT Cerebellum mRNA M430 (Oct04) MAS5"
+               ],
+               [
                   "CB_M_1003_M",
                   "SJUT Cerebellum mRNA M430 (Oct03) MAS5"
                ],
@@ -1552,10 +1548,6 @@
             ],
             "Prefrontal Cortex mRNA": [
                [
-                  "VCUEtOH_1206_R",
-                  "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA"
-               ],
-               [
                   "VCUSal_1206_R",
                   "VCU BXD PFC Sal M430 2.0 (Dec06) RMA"
                ],
@@ -1730,10 +1722,6 @@
                   "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
                ],
                [
-                  "VCUEtOH_0609_R",
-                  "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
-               ],
-               [
                   "VCUSal_0609_R",
                   "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **"
                ],
@@ -2018,10 +2006,6 @@
                   "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
                ],
                [
-                  "VCUEtOH_0806_R",
-                  "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
-               ],
-               [
                   "VCUSal_0806_R",
                   "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA"
                ],
@@ -2572,7 +2556,7 @@
             ],
             [
                "Leaf mRNA",
-               "Leaf mRNA mRNA"
+               "Leaf mRNA"
             ]
          ],
          "SXM": [
@@ -2586,11 +2570,11 @@
             ],
             [
                "Embryo mRNA",
-               "Embryo mRNA mRNA"
+               "Embryo mRNA"
             ],
             [
                "Leaf mRNA",
-               "Leaf mRNA mRNA"
+               "Leaf mRNA"
             ]
          ]
       },
@@ -2606,7 +2590,7 @@
             ],
             [
                "Whole Body mRNA",
-               "Whole Body mRNA mRNA"
+               "Whole Body mRNA"
             ]
          ],
          "Oregon-R_x_2b3": [
@@ -2620,7 +2604,7 @@
             ],
             [
                "Whole Body mRNA",
-               "Whole Body mRNA mRNA"
+               "Whole Body mRNA"
             ]
          ]
       },
@@ -2636,7 +2620,7 @@
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ]
          ],
          "AD-cases-controls-Myers": [
@@ -2650,7 +2634,7 @@
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ]
          ],
          "CANDLE": [
@@ -2664,11 +2648,11 @@
             ],
             [
                "Methylation",
-               "Methylation mRNA"
+               "Methylation"
             ],
             [
                "Newborn Cord Blood mRNA",
-               "Newborn Cord Blood mRNA mRNA"
+               "Newborn Cord Blood mRNA"
             ]
          ],
          "CEPH-2004": [
@@ -2682,7 +2666,7 @@
             ],
             [
                "Lymphoblast B-cell mRNA",
-               "Lymphoblast B-cell mRNA mRNA"
+               "Lymphoblast B-cell mRNA"
             ]
          ],
          "HB": [
@@ -2696,15 +2680,15 @@
             ],
             [
                "Cerebellum mRNA",
-               "Cerebellum mRNA mRNA"
+               "Cerebellum mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA mRNA"
+               "Prefrontal Cortex mRNA"
             ],
             [
                "Primary Visual Cortex mRNA",
-               "Primary Visual Cortex mRNA mRNA"
+               "Primary Visual Cortex mRNA"
             ]
          ],
          "HLC": [
@@ -2718,7 +2702,7 @@
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ]
          ],
          "HLT": [
@@ -2732,7 +2716,7 @@
             ],
             [
                "Lung mRNA",
-               "Lung mRNA mRNA"
+               "Lung mRNA"
             ]
          ],
          "HSB": [
@@ -2746,67 +2730,67 @@
             ],
             [
                "Amygdala mRNA",
-               "Amygdala mRNA mRNA"
+               "Amygdala mRNA"
             ],
             [
                "Cerebellar Cortex mRNA",
-               "Cerebellar Cortex mRNA mRNA"
+               "Cerebellar Cortex mRNA"
             ],
             [
                "Dorsolateral Prefrontal Cortex mRNA",
-               "Dorsolateral Prefrontal Cortex mRNA mRNA"
+               "Dorsolateral Prefrontal Cortex mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Inferior Temporal Cortex mRNA",
-               "Inferior Temporal Cortex mRNA mRNA"
+               "Inferior Temporal Cortex mRNA"
             ],
             [
                "Medial Prefrontal Cortex mRNA",
-               "Medial Prefrontal Cortex mRNA mRNA"
+               "Medial Prefrontal Cortex mRNA"
             ],
             [
                "Mediodorsal Nucleus of Thalamus mRNA",
-               "Mediodorsal Nucleus of Thalamus mRNA mRNA"
+               "Mediodorsal Nucleus of Thalamus mRNA"
             ],
             [
                "Orbital Prefrontal Cortex mRNA",
-               "Orbital Prefrontal Cortex mRNA mRNA"
+               "Orbital Prefrontal Cortex mRNA"
             ],
             [
                "Posterior Inferior Parietal Cortex mRNA",
-               "Posterior Inferior Parietal Cortex mRNA mRNA"
+               "Posterior Inferior Parietal Cortex mRNA"
             ],
             [
                "Posterior Superior Temporal Cortex mRNA",
-               "Posterior Superior Temporal Cortex mRNA mRNA"
+               "Posterior Superior Temporal Cortex mRNA"
             ],
             [
                "Primary Auditory (A1) Cortex mRNA",
-               "Primary Auditory (A1) Cortex mRNA mRNA"
+               "Primary Auditory (A1) Cortex mRNA"
             ],
             [
                "Primary Motor (M1) Cortex mRNA",
-               "Primary Motor (M1) Cortex mRNA mRNA"
+               "Primary Motor (M1) Cortex mRNA"
             ],
             [
                "Primary Somatosensory (S1) Cortex mRNA",
-               "Primary Somatosensory (S1) Cortex mRNA mRNA"
+               "Primary Somatosensory (S1) Cortex mRNA"
             ],
             [
                "Primary Visual Cortex mRNA",
-               "Primary Visual Cortex mRNA mRNA"
+               "Primary Visual Cortex mRNA"
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA mRNA"
+               "Striatum mRNA"
             ],
             [
                "Ventrolateral Prefrontal Cortex mRNA",
-               "Ventrolateral Prefrontal Cortex mRNA mRNA"
+               "Ventrolateral Prefrontal Cortex mRNA"
             ]
          ]
       },
@@ -2822,23 +2806,23 @@
             ],
             [
                "Amygdala mRNA",
-               "Amygdala mRNA mRNA"
+               "Amygdala mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Nucleus Accumbens mRNA",
-               "Nucleus Accumbens mRNA mRNA"
+               "Nucleus Accumbens mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA mRNA"
+               "Prefrontal Cortex mRNA"
             ]
          ]
       },
@@ -2854,7 +2838,7 @@
             ],
             [
                "Mammary Tumors mRNA",
-               "Mammary Tumors mRNA mRNA"
+               "Mammary Tumors mRNA"
             ]
          ],
          "AXBXA": [
@@ -2868,19 +2852,19 @@
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA mRNA"
+               "Bone Femur mRNA"
             ],
             [
                "Eye mRNA",
-               "Eye mRNA mRNA"
+               "Eye mRNA"
             ],
             [
                "Heart mRNA",
-               "Heart mRNA mRNA"
+               "Heart mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ]
          ],
          "B6BTBRF2": [
@@ -2894,7 +2878,7 @@
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ]
          ],
          "B6D2F2": [
@@ -2908,7 +2892,7 @@
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ]
          ],
          "B6D2F2-PSU": [
@@ -2922,7 +2906,7 @@
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA mRNA"
+               "Muscle mRNA"
             ]
          ],
          "B6D2RI": [
@@ -2936,7 +2920,7 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ]
          ],
          "BDF2-1999": [
@@ -2950,7 +2934,7 @@
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ]
          ],
          "BDF2-2005": [
@@ -2964,7 +2948,7 @@
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA mRNA"
+               "Striatum mRNA"
             ]
          ],
          "BHF2": [
@@ -2978,19 +2962,19 @@
             ],
             [
                "Adipose mRNA",
-               "Adipose mRNA mRNA"
+               "Adipose mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA mRNA"
+               "Muscle mRNA"
             ]
          ],
          "BHHBF2": [
@@ -3004,19 +2988,19 @@
             ],
             [
                "Adipose mRNA",
-               "Adipose mRNA mRNA"
+               "Adipose mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA mRNA"
+               "Muscle mRNA"
             ]
          ],
          "BXD": [
@@ -3030,119 +3014,119 @@
             ],
             [
                "Adrenal Gland mRNA",
-               "Adrenal Gland mRNA mRNA"
+               "Adrenal Gland mRNA"
             ],
             [
                "Amygdala mRNA",
-               "Amygdala mRNA mRNA"
+               "Amygdala mRNA"
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA mRNA"
+               "Bone Femur mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ],
             [
                "Cartilage mRNA",
-               "Cartilage mRNA mRNA"
+               "Cartilage mRNA"
             ],
             [
                "Cerebellum mRNA",
-               "Cerebellum mRNA mRNA"
+               "Cerebellum mRNA"
             ],
             [
                "Eye mRNA",
-               "Eye mRNA mRNA"
+               "Eye mRNA"
             ],
             [
                "Hematopoietic Cells mRNA",
-               "Hematopoietic Cells mRNA mRNA"
+               "Hematopoietic Cells mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Hypothalamus mRNA",
-               "Hypothalamus mRNA mRNA"
+               "Hypothalamus mRNA"
             ],
             [
                "Kidney mRNA",
-               "Kidney mRNA mRNA"
+               "Kidney mRNA"
             ],
             [
                "Leucocytes mRNA",
-               "Leucocytes mRNA mRNA"
+               "Leucocytes mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ],
             [
                "Liver Proteome",
-               "Liver Proteome mRNA"
+               "Liver Proteome"
             ],
             [
                "Lung mRNA",
-               "Lung mRNA mRNA"
+               "Lung mRNA"
             ],
             [
                "Midbrain mRNA",
-               "Midbrain mRNA mRNA"
+               "Midbrain mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA mRNA"
+               "Muscle mRNA"
             ],
             [
                "Neocortex mRNA",
-               "Neocortex mRNA mRNA"
+               "Neocortex mRNA"
             ],
             [
                "Nucleus Accumbens mRNA",
-               "Nucleus Accumbens mRNA mRNA"
+               "Nucleus Accumbens mRNA"
             ],
             [
                "Pituitary Gland mRNA",
-               "Pituitary Gland mRNA mRNA"
+               "Pituitary Gland mRNA"
             ],
             [
                "Popliteal Lymph Node mRNA",
-               "Popliteal Lymph Node mRNA mRNA"
+               "Popliteal Lymph Node mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA mRNA"
+               "Prefrontal Cortex mRNA"
             ],
             [
                "Retina mRNA",
-               "Retina mRNA mRNA"
+               "Retina mRNA"
             ],
             [
                "Spleen mRNA",
-               "Spleen mRNA mRNA"
+               "Spleen mRNA"
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA mRNA"
+               "Striatum mRNA"
             ],
             [
                "T Cell (helper) mRNA",
-               "T Cell (helper) mRNA mRNA"
+               "T Cell (helper) mRNA"
             ],
             [
                "T Cell (regulatory) mRNA",
-               "T Cell (regulatory) mRNA mRNA"
+               "T Cell (regulatory) mRNA"
             ],
             [
                "Thymus mRNA",
-               "Thymus mRNA mRNA"
+               "Thymus mRNA"
             ],
             [
                "Ventral Tegmental Area mRNA",
-               "Ventral Tegmental Area mRNA mRNA"
+               "Ventral Tegmental Area mRNA"
             ]
          ],
          "BXH": [
@@ -3156,15 +3140,15 @@
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA mRNA"
+               "Bone Femur mRNA"
             ],
             [
                "Cartilage mRNA",
-               "Cartilage mRNA mRNA"
+               "Cartilage mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ]
          ],
          "C57BL-6JxC57BL-6NJF2": [
@@ -3188,19 +3172,19 @@
             ],
             [
                "Adipose mRNA",
-               "Adipose mRNA mRNA"
+               "Adipose mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA mRNA"
+               "Brain mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA mRNA"
+               "Muscle mRNA"
             ]
          ],
          "CXB": [
@@ -3214,11 +3198,11 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Spleen mRNA",
-               "Spleen mRNA mRNA"
+               "Spleen mRNA"
             ]
          ],
          "HS": [
@@ -3232,15 +3216,15 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ],
             [
                "Lung mRNA",
-               "Lung mRNA mRNA"
+               "Lung mRNA"
             ]
          ],
          "HS-CC": [
@@ -3254,7 +3238,7 @@
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA mRNA"
+               "Striatum mRNA"
             ]
          ],
          "LXS": [
@@ -3268,11 +3252,11 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA mRNA"
+               "Prefrontal Cortex mRNA"
             ]
          ],
          "MDP": [
@@ -3286,19 +3270,19 @@
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA mRNA"
+               "Bone Femur mRNA"
             ],
             [
                "Dorsal Root Ganglia mRNA",
-               "Dorsal Root Ganglia mRNA mRNA"
+               "Dorsal Root Ganglia mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ]
          ],
          "NZBXFVB-N2": [
@@ -3312,7 +3296,7 @@
             ],
             [
                "Mammary Tumors mRNA",
-               "Mammary Tumors mRNA mRNA"
+               "Mammary Tumors mRNA"
             ]
          ],
          "SOTNOT-OHSU": [
@@ -3336,7 +3320,7 @@
             ],
             [
                "Anterior Cingulate Cortex mRNA",
-               "Anterior Cingulate Cortex mRNA mRNA"
+               "Anterior Cingulate Cortex mRNA"
             ]
          ]
       },
@@ -3362,27 +3346,27 @@
             ],
             [
                "Adrenal Gland mRNA",
-               "Adrenal Gland mRNA mRNA"
+               "Adrenal Gland mRNA"
             ],
             [
                "Heart mRNA",
-               "Heart mRNA mRNA"
+               "Heart mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA mRNA"
+               "Hippocampus mRNA"
             ],
             [
                "Kidney mRNA",
-               "Kidney mRNA mRNA"
+               "Kidney mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA mRNA"
+               "Liver mRNA"
             ],
             [
                "Peritoneal Fat mRNA",
-               "Peritoneal Fat mRNA mRNA"
+               "Peritoneal Fat mRNA"
             ]
          ],
          "SRxSHRSPF2": [
@@ -3396,7 +3380,7 @@
             ],
             [
                "Eye mRNA",
-               "Eye mRNA mRNA"
+               "Eye mRNA"
             ]
          ]
       },