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-rw-r--r--templates/topAddictionGene.html355
-rwxr-xr-x[-rw-r--r--]topGene_step0_extract_gene_alias_from_gene_info.sh (renamed from extract_gene_symb_name_from_ncbi_gene_info.sh)0
-rwxr-xr-xtopGene_step1_cnt_abstracts.py57
-rwxr-xr-xtopGene_step2_cnt_sentences.py16
-rwxr-xr-xtopGene_step3_generate_html.py15
-rwxr-xr-xtopGene_step4_get_pmids_for_all_top_genes.py33
6 files changed, 288 insertions, 188 deletions
diff --git a/templates/topAddictionGene.html b/templates/topAddictionGene.html
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--- a/templates/topAddictionGene.html
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+
{% extends "layout.html" %}
{% block content %}
-<h3> Top 150 addiction related genes </h3>
+<h3> Top addiction related genes </h3>
<br>
These genes are ranked by the number of PubMed abstracts that contain the name of the gene and one or more addiction related keyword.
<hr>
-<ol>
+<ol><li><a href="/showTopGene?topGene=CNR1">CNR1</a> <span style="font-size:small; color:grey">(CNRS1; PROTOCADHERIN ALPHA CLUSTER, COMPLEX LOCUS)</span><br>
+<li><a href="/showTopGene?topGene=OPRM1">OPRM1</a> <span style="font-size:small; color:grey">(LMOR; M-OR-1; MOP; MOR; MOR1; OPRM; OPIOID RECEPTOR MU 1)</span><br>
+<li><a href="/showTopGene?topGene=FOS">FOS</a> <span style="font-size:small; color:grey">(C-FOS; P55; FOS PROTO-ONCOGENE, AP-1 TRANSCRIPTION FACTOR SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=SLC6A3">SLC6A3</a> <span style="font-size:small; color:grey">(DAT; DAT1; PKDYS; PKDYS1; SOLUTE CARRIER FAMILY 6 MEMBER 3)</span><br>
+<li><a href="/showTopGene?topGene=CRH">CRH</a> <span style="font-size:small; color:grey">(CRF; CRH1; CORTICOTROPIN RELEASING HORMONE)</span><br>
+<li><a href="/showTopGene?topGene=BDNF">BDNF</a> <span style="font-size:small; color:grey">(ANON2; BULN2; BRAIN DERIVED NEUROTROPHIC FACTOR)</span><br>
+<li><a href="/showTopGene?topGene=DRD2">DRD2</a> <span style="font-size:small; color:grey">(D2DR; D2R; DOPAMINE RECEPTOR D2)</span><br>
+<li><a href="/showTopGene?topGene=POMC">POMC</a> <span style="font-size:small; color:grey">(ACTH; OBAIRH; PROOPIOMELANOCORTIN)</span><br>
+<li><a href="/showTopGene?topGene=CREB1">CREB1</a> <span style="font-size:small; color:grey">(CREB; CREB-1; CAMP RESPONSIVE ELEMENT BINDING PROTEIN 1)</span><br>
+<li><a href="/showTopGene?topGene=OPRK1">OPRK1</a> <span style="font-size:small; color:grey">(K-OR-1; KOR; KOR-1; OPRK; OPIOID RECEPTOR KAPPA 1)</span><br>
+<li><a href="/showTopGene?topGene=TNF">TNF</a> <span style="font-size:small; color:grey">(TNF-ALPHA; TNFA; TNFSF2; TNLG1F; TUMOR NECROSIS FACTOR)</span><br>
+<li><a href="/showTopGene?topGene=MAPK1">MAPK1</a> <span style="font-size:small; color:grey">(ERK; ERK-2; ERK2; ERT1; MAPK2; P42MAPK; PRKM1; PRKM2; P41; P41MAPK; P42-MAPK; MITOGEN-ACTIVATED PROTEIN KINASE 1)</span><br>
+<li><a href="/showTopGene?topGene=SLC6A4">SLC6A4</a> <span style="font-size:small; color:grey">(5-HTT; 5-HTTLPR; 5HTT; OCD1; SERT; SERT1; HSERT; SOLUTE CARRIER FAMILY 6 MEMBER 4)</span><br>
+<li><a href="/showTopGene?topGene=CNR2">CNR2</a> <span style="font-size:small; color:grey">(CB-2; CB2; CX5; CANNABINOID RECEPTOR 2)</span><br>
+<li><a href="/showTopGene?topGene=OXT">OXT</a> <span style="font-size:small; color:grey">(OT-NPI; OXT-NPI; OXYTOCIN; NEUROPHYSIN I PREPROPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=GRM5">GRM5</a> <span style="font-size:small; color:grey">(GPRC1E; MGLUR5; PPP1R86; MGLU5; GLUTAMATE METABOTROPIC RECEPTOR 5)</span><br>
+<li><a href="/showTopGene?topGene=NPY">NPY</a> <span style="font-size:small; color:grey">(PYY4; NEUROPEPTIDE Y)</span><br>
+<li><a href="/showTopGene?topGene=NOS1">NOS1</a> <span style="font-size:small; color:grey">(IHPS1; N-NOS; NC-NOS; NOS; BNOS; NNOS; NITRIC OXIDE SYNTHASE 1)</span><br>
+<li><a href="/showTopGene?topGene=ALDH2">ALDH2</a> <span style="font-size:small; color:grey">(ALDH-E2; ALDHI; ALDM; ALDEHYDE DEHYDROGENASE 2 FAMILY MEMBER)</span><br>
+<li><a href="/showTopGene?topGene=PNOC">PNOC</a> <span style="font-size:small; color:grey">(NOP; OFQ; PPNOC; PREPRONOCICEPTIN)</span><br>
+<li><a href="/showTopGene?topGene=GRIA1">GRIA1</a> <span style="font-size:small; color:grey">(GLUH1; GLUR1; GLURA; GLUA1; HBGR1; GLUTAMATE IONOTROPIC RECEPTOR AMPA TYPE SUBUNIT 1)</span><br>
+<li><a href="/showTopGene?topGene=CHRNA5">CHRNA5</a> <span style="font-size:small; color:grey">(LNCR2; CHOLINERGIC RECEPTOR NICOTINIC ALPHA 5 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=GRIN2B">GRIN2B</a> <span style="font-size:small; color:grey">(EIEE27; GLUN2B; MRD6; NMDAR2B; NR2B; NR3; HNR3; GLUTAMATE IONOTROPIC RECEPTOR NMDA TYPE SUBUNIT 2B)</span><br>
+<li><a href="/showTopGene?topGene=IL6">IL6</a> <span style="font-size:small; color:grey">(BSF-2; BSF2; HGF; HSF; IFN-BETA-2; IFNB2; IL-6; INTERLEUKIN 6)</span><br>
+<li><a href="/showTopGene?topGene=PDYN">PDYN</a> <span style="font-size:small; color:grey">(ADCA; PENKB; SCA23; PRODYNORPHIN)</span><br>
+<li><a href="/showTopGene?topGene=GRM2">GRM2</a> <span style="font-size:small; color:grey">(GLUR2; GPRC1B; MGLUR2; MGLU2; GLUTAMATE METABOTROPIC RECEPTOR 2)</span><br>
+<li><a href="/showTopGene?topGene=HTR1A">HTR1A</a> <span style="font-size:small; color:grey">(5-HT-1A; 5-HT1A; 5HT1A; ADRB2RL1; ADRBRL1; PFMCD; 5-HYDROXYTRYPTAMINE RECEPTOR 1A)</span><br>
+<li><a href="/showTopGene?topGene=COMT">COMT</a> <span style="font-size:small; color:grey">(HEL-S-98N; CATECHOL-O-METHYLTRANSFERASE)</span><br>
+<li><a href="/showTopGene?topGene=CRHR1">CRHR1</a> <span style="font-size:small; color:grey">(CRF-R; CRF-R-1; CRF-R1; CRF1; CRFR-1; CRFR1; CRH-R-1; CRH-R1; CRHR; CRHR1L; CORTICOTROPIN RELEASING HORMONE RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=GGT1">GGT1</a> <span style="font-size:small; color:grey">(CD224; D22S672; D22S732; GGT; GGT 1; GGTD; GAMMA-GLUTAMYLTRANSFERASE 1)</span><br>
+<li><a href="/showTopGene?topGene=MAPK3">MAPK3</a> <span style="font-size:small; color:grey">(ERK-1; ERK1; ERT2; HS44KDAP; HUMKER1A; P44ERK1; P44MAPK; PRKM3; P44-ERK1; P44-MAPK; MITOGEN-ACTIVATED PROTEIN KINASE 3)</span><br>
+<li><a href="/showTopGene?topGene=CYP2A6">CYP2A6</a> <span style="font-size:small; color:grey">(CPA6; CYP2A; CYP2A3; CYPIIA6; P450C2A; P450PB; CYTOCHROME P450 FAMILY 2 SUBFAMILY A MEMBER 6)</span><br>
+<li><a href="/showTopGene?topGene=ADH1B">ADH1B</a> <span style="font-size:small; color:grey">(ADH2; HEL-S-117; ALCOHOL DEHYDROGENASE 1B CLASS I , BETA POLYPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=GRIN1">GRIN1</a> <span style="font-size:small; color:grey">(GLUN1; MRD8; NDHMSD; NDHMSR; NMD-R1; NMDA1; NMDAR1; NR1; GLUTAMATE IONOTROPIC RECEPTOR NMDA TYPE SUBUNIT 1)</span><br>
+<li><a href="/showTopGene?topGene=DRD4">DRD4</a> <span style="font-size:small; color:grey">(D4DR; DOPAMINE RECEPTOR D4)</span><br>
+<li><a href="/showTopGene?topGene=NPS">NPS</a> <span style="font-size:small; color:grey">(NEUROPEPTIDE S)</span><br>
+<li><a href="/showTopGene?topGene=HTR2A">HTR2A</a> <span style="font-size:small; color:grey">(5-HT2A; HTR2; 5-HYDROXYTRYPTAMINE RECEPTOR 2A)</span><br>
+<li><a href="/showTopGene?topGene=GAD1">GAD1</a> <span style="font-size:small; color:grey">(CPSQ1; GAD; SCP; GLUTAMATE DECARBOXYLASE 1)</span><br>
+<li><a href="/showTopGene?topGene=PENK">PENK</a> <span style="font-size:small; color:grey">(PENK-A; PROENKEPHALIN)</span><br>
+<li><a href="/showTopGene?topGene=GRIA2">GRIA2</a> <span style="font-size:small; color:grey">(GLUR2; GLURB; GLUA2; GLUR-K2; HBGR2; GLUTAMATE IONOTROPIC RECEPTOR AMPA TYPE SUBUNIT 2)</span><br>
+<li><a href="/showTopGene?topGene=TLR4">TLR4</a> <span style="font-size:small; color:grey">(ARMD10; CD284; TLR-4; TOLL LIKE RECEPTOR 4)</span><br>
+<li><a href="/showTopGene?topGene=MAOA">MAOA</a> <span style="font-size:small; color:grey">(BRNRS; MAO-A; MONOAMINE OXIDASE A)</span><br>
+<li><a href="/showTopGene?topGene=ARC">ARC</a> <span style="font-size:small; color:grey">(ARG3.1; HARC; ACTIVITY REGULATED CYTOSKELETON ASSOCIATED PROTEIN)</span><br>
+<li><a href="/showTopGene?topGene=CHRNA3">CHRNA3</a> <span style="font-size:small; color:grey">(LNCR2; NACHRA3; PAOD2; CHOLINERGIC RECEPTOR NICOTINIC ALPHA 3 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=FOSB">FOSB</a> <span style="font-size:small; color:grey">(G0S3; GOS3; GOSB; FOSB PROTO-ONCOGENE, AP-1 TRANSCRIPTION FACTOR SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=CYP2E1">CYP2E1</a> <span style="font-size:small; color:grey">(CPE1; CYP2E; P450-J; P450C2E; CYTOCHROME P450 FAMILY 2 SUBFAMILY E MEMBER 1)</span><br>
+<li><a href="/showTopGene?topGene=TRPV1">TRPV1</a> <span style="font-size:small; color:grey">(TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL SUBFAMILY V MEMBER 1)</span><br>
+<li><a href="/showTopGene?topGene=IFNA1">IFNA1</a> <span style="font-size:small; color:grey">(IFL; IFN; IFN-ALPHA; IFN-ALPHAD; IFNA13; IFNA@; INTERFERON ALPHA 1)</span><br>
+<li><a href="/showTopGene?topGene=HTR2C">HTR2C</a> <span style="font-size:small; color:grey">(5-HT1C; 5-HT2C; 5-HTR2C; 5HTR2C; HTR1C; 5-HYDROXYTRYPTAMINE RECEPTOR 2C)</span><br>
+<li><a href="/showTopGene?topGene=DBH">DBH</a> <span style="font-size:small; color:grey">(ORTHYP1; DOPAMINE BETA-HYDROXYLASE)</span><br>
+<li><a href="/showTopGene?topGene=NGF">NGF</a> <span style="font-size:small; color:grey">(BETA-NGF; HSAN5; NGFB; NERVE GROWTH FACTOR)</span><br>
+<li><a href="/showTopGene?topGene=GABRA2">GABRA2</a> <span style="font-size:small; color:grey">(GAMMA-AMINOBUTYRIC ACID TYPE A RECEPTOR ALPHA2 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=NTRK2">NTRK2</a> <span style="font-size:small; color:grey">(EIEE58; GP145-TRKB; OBHD; TRKB; TRK-B; NEUROTROPHIC RECEPTOR TYROSINE KINASE 2)</span><br>
+<li><a href="/showTopGene?topGene=SLC1A2">SLC1A2</a> <span style="font-size:small; color:grey">(EAAT2; EIEE41; GLT-1; HBGT; SOLUTE CARRIER FAMILY 1 MEMBER 2)</span><br>
+<li><a href="/showTopGene?topGene=GRIN2A">GRIN2A</a> <span style="font-size:small; color:grey">(EPND; FESD; GLUN2A; LKS; NMDAR2A; NR2A; GLUTAMATE IONOTROPIC RECEPTOR NMDA TYPE SUBUNIT 2A)</span><br>
+<li><a href="/showTopGene?topGene=CRP">CRP</a> <span style="font-size:small; color:grey">(PTX1; C-REACTIVE PROTEIN)</span><br>
+<li><a href="/showTopGene?topGene=HTR1B">HTR1B</a> <span style="font-size:small; color:grey">(5-HT-1B; 5-HT-1D-BETA; 5-HT1B; 5-HT1DB; HTR1D2; HTR1DB; 5-HYDROXYTRYPTAMINE RECEPTOR 1B)</span><br>
+<li><a href="/showTopGene?topGene=ANKK1">ANKK1</a> <span style="font-size:small; color:grey">(PKK2; SGK288; ANKYRIN REPEAT AND KINASE DOMAIN CONTAINING 1)</span><br>
+<li><a href="/showTopGene?topGene=OPRD1">OPRD1</a> <span style="font-size:small; color:grey">(DOP; DOR1; OPRD; OPIOID RECEPTOR DELTA 1)</span><br>
+<li><a href="/showTopGene?topGene=GFAP">GFAP</a> <span style="font-size:small; color:grey">(ALXDRD; GLIAL FIBRILLARY ACIDIC PROTEIN)</span><br>
+<li><a href="/showTopGene?topGene=CHRNB4">CHRNB4</a> <span style="font-size:small; color:grey">(CHOLINERGIC RECEPTOR NICOTINIC BETA 4 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=CALCA">CALCA</a> <span style="font-size:small; color:grey">(CALC1; CGRP; CGRP-I; CGRP1; PCT; CALCITONIN RELATED POLYPEPTIDE ALPHA)</span><br>
+<li><a href="/showTopGene?topGene=IL10">IL10</a> <span style="font-size:small; color:grey">(CSIF; GVHDS; IL-10; IL10A; TGIF; INTERLEUKIN 10)</span><br>
+<li><a href="/showTopGene?topGene=JUN">JUN</a> <span style="font-size:small; color:grey">(AP1; C-JUN; JUN PROTO-ONCOGENE, AP-1 TRANSCRIPTION FACTOR SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=PSENEN">PSENEN</a> <span style="font-size:small; color:grey">(ACNINV2; MDS033; MSTP064; PEN-2; PEN2; PRESENILIN ENHANCER, GAMMA-SECRETASE SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=PTGS2">PTGS2</a> <span style="font-size:small; color:grey">(COX-2; COX2; GRIPGHS; PGG/HS; PGHS-2; PHS-2; HCOX-2; PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 2)</span><br>
+<li><a href="/showTopGene?topGene=CYP3A4">CYP3A4</a> <span style="font-size:small; color:grey">(CP33; CP34; CYP3A; CYP3A3; CYPIIIA3; CYPIIIA4; HLP; NF-25; P450C3; P450PCN1; CYTOCHROME P450 FAMILY 3 SUBFAMILY A MEMBER 4)</span><br>
+<li><a href="/showTopGene?topGene=ADH1C">ADH1C</a> <span style="font-size:small; color:grey">(ADH3; ALCOHOL DEHYDROGENASE 1C CLASS I , GAMMA POLYPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=GDNF">GDNF</a> <span style="font-size:small; color:grey">(ATF1; ATF2; HFB1-GDNF; HSCR3; GLIAL CELL DERIVED NEUROTROPHIC FACTOR)</span><br>
+<li><a href="/showTopGene?topGene=GRM1">GRM1</a> <span style="font-size:small; color:grey">(GPRC1A; MGLU1; MGLUR1; PPP1R85; SCA44; SCAR13; GLUTAMATE METABOTROPIC RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=DRD1">DRD1</a> <span style="font-size:small; color:grey">(DADR; DRD1A; DOPAMINE RECEPTOR D1)</span><br>
+<li><a href="/showTopGene?topGene=MTOR">MTOR</a> <span style="font-size:small; color:grey">(FRAP; FRAP1; FRAP2; RAFT1; RAPT1; SKS; MECHANISTIC TARGET OF RAPAMYCIN KINASE)</span><br>
+<li><a href="/showTopGene?topGene=BCHE">BCHE</a> <span style="font-size:small; color:grey">(BCHED; CHE1; CHE2; BUTYRYLCHOLINESTERASE)</span><br>
+<li><a href="/showTopGene?topGene=PPARA">PPARA</a> <span style="font-size:small; color:grey">(NR1C1; PPAR; PPARALPHA; HPPAR; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA)</span><br>
+<li><a href="/showTopGene?topGene=TRH">TRH</a> <span style="font-size:small; color:grey">(PRO-TRH; THYROTROPIN RELEASING HORMONE)</span><br>
+<li><a href="/showTopGene?topGene=OPRL1">OPRL1</a> <span style="font-size:small; color:grey">(KOR-3; NOCIR; NOPR; ORL1; OPIOID RELATED NOCICEPTIN RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=IL2">IL2</a> <span style="font-size:small; color:grey">(IL-2; TCGF; INTERLEUKIN 2)</span><br>
+<li><a href="/showTopGene?topGene=RTN4">RTN4</a> <span style="font-size:small; color:grey">(NOGO; NSP; NSP-CL; NBLA00271; NBLA10545; RTN-X; RTN4-A; RTN4-B1; RTN4-B2; RTN4-C; RETICULON 4)</span><br>
+<li><a href="/showTopGene?topGene=PPP1R1B">PPP1R1B</a> <span style="font-size:small; color:grey">(DARPP-32; DARPP32; PROTEIN PHOSPHATASE 1 REGULATORY INHIBITOR SUBUNIT 1B)</span><br>
+<li><a href="/showTopGene?topGene=DRD3">DRD3</a> <span style="font-size:small; color:grey">(D3DR; ETM1; FET1; DOPAMINE RECEPTOR D3)</span><br>
+<li><a href="/showTopGene?topGene=CYP2B6">CYP2B6</a> <span style="font-size:small; color:grey">(CPB6; CYP2B; CYP2B7; CYP2B7P; CYPIIB6; EFVM; IIB1; CYTOCHROME P450 FAMILY 2 SUBFAMILY B MEMBER 6)</span><br>
+<li><a href="/showTopGene?topGene=ABCB1">ABCB1</a> <span style="font-size:small; color:grey">(ABC20; CD243; CLCS; GP170; MDR1; P-GP; PGY1; ATP BINDING CASSETTE SUBFAMILY B MEMBER 1)</span><br>
+<li><a href="/showTopGene?topGene=MGLL">MGLL</a> <span style="font-size:small; color:grey">(HU-K5; HUK5; MAGL; MGL; MONOGLYCERIDE LIPASE)</span><br>
+<li><a href="/showTopGene?topGene=CCL2">CCL2</a> <span style="font-size:small; color:grey">(GDCF-2; HC11; HSMCR30; MCAF; MCP-1; MCP1; SCYA2; SMC-CF; C-C MOTIF CHEMOKINE LIGAND 2)</span><br>
+<li><a href="/showTopGene?topGene=NOS2">NOS2</a> <span style="font-size:small; color:grey">(HEP-NOS; INOS; NOS2A; NITRIC OXIDE SYNTHASE 2)</span><br>
+<li><a href="/showTopGene?topGene=EGFR">EGFR</a> <span style="font-size:small; color:grey">(ERBB; ERBB1; HER1; NISBD2; PIG61; MENA; EPIDERMAL GROWTH FACTOR RECEPTOR)</span><br>
+<li><a href="/showTopGene?topGene=HOMER1">HOMER1</a> <span style="font-size:small; color:grey">(HOMER; HOMER1A; HOMER1B; HOMER1C; SYN47; VES-1; HOMER SCAFFOLD PROTEIN 1)</span><br>
+<li><a href="/showTopGene?topGene=BCL2">BCL2</a> <span style="font-size:small; color:grey">(BCL-2; PPP1R50; BCL2 APOPTOSIS REGULATOR)</span><br>
+<li><a href="/showTopGene?topGene=PLAT">PLAT</a> <span style="font-size:small; color:grey">(T-PA; TPA; PLASMINOGEN ACTIVATOR, TISSUE TYPE)</span><br>
+<li><a href="/showTopGene?topGene=IL1B">IL1B</a> <span style="font-size:small; color:grey">(IL-1; IL1-BETA; IL1F2; INTERLEUKIN 1 BETA)</span><br>
+<li><a href="/showTopGene?topGene=HCRTR1">HCRTR1</a> <span style="font-size:small; color:grey">(OX1R; HYPOCRETIN RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=CDK5">CDK5</a> <span style="font-size:small; color:grey">(LIS7; PSSALRE; CYCLIN DEPENDENT KINASE 5)</span><br>
+<li><a href="/showTopGene?topGene=ADA2">ADA2</a> <span style="font-size:small; color:grey">(ADGF; CECR1; IDGFL; PAN; SNEDS; VAIHS; ADENOSINE DEAMINASE 2)</span><br>
+<li><a href="/showTopGene?topGene=CHAT">CHAT</a> <span style="font-size:small; color:grey">(CHOACTASE; CMS1A; CMS1A2; CMS6; CHOLINE O-ACETYLTRANSFERASE)</span><br>
+<li><a href="/showTopGene?topGene=MAP2K7">MAP2K7</a> <span style="font-size:small; color:grey">(JNKK2; MAPKK7; MEK; MEK 7; MKK7; PRKMK7; SAPKK-4; SAPKK4; MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7)</span><br>
+<li><a href="/showTopGene?topGene=IL4">IL4</a> <span style="font-size:small; color:grey">(BCGF-1; BCGF1; BSF-1; BSF1; IL-4; INTERLEUKIN 4)</span><br>
+<li><a href="/showTopGene?topGene=BAX">BAX</a> <span style="font-size:small; color:grey">(BCL2L4; BCL2 ASSOCIATED X, APOPTOSIS REGULATOR)</span><br>
+<li><a href="/showTopGene?topGene=SLC18A2">SLC18A2</a> <span style="font-size:small; color:grey">(PKDYS2; SVAT; SVMT; VAT2; VMAT2; SOLUTE CARRIER FAMILY 18 MEMBER A2)</span><br>
+<li><a href="/showTopGene?topGene=MAPK8">MAPK8</a> <span style="font-size:small; color:grey">(JNK; JNK-46; JNK1; JNK1A2; JNK21B1/2; PRKM8; SAPK1; SAPK1C; MITOGEN-ACTIVATED PROTEIN KINASE 8)</span><br>
+<li><a href="/showTopGene?topGene=ADORA2A">ADORA2A</a> <span style="font-size:small; color:grey">(A2AR; ADORA2; RDC8; ADENOSINE A2A RECEPTOR)</span><br>
+<li><a href="/showTopGene?topGene=PIK3CD">PIK3CD</a> <span style="font-size:small; color:grey">(APDS; IMD14; P110DELTA; PI3K; P110D; PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA)</span><br>
+<li><a href="/showTopGene?topGene=CHRNA4">CHRNA4</a> <span style="font-size:small; color:grey">(BFNC; EBN1; NACHRA4; NACRA4; CHOLINERGIC RECEPTOR NICOTINIC ALPHA 4 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=SRC">SRC</a> <span style="font-size:small; color:grey">(SRC1; THC6; C-SRC; P60-SRC; SRC PROTO-ONCOGENE, NON-RECEPTOR TYROSINE KINASE)</span><br>
+<li><a href="/showTopGene?topGene=NPFF">NPFF</a> <span style="font-size:small; color:grey">(FMRFAL; NEUROPEPTIDE FF-AMIDE PEPTIDE PRECURSOR)</span><br>
+<li><a href="/showTopGene?topGene=HOMER2">HOMER2</a> <span style="font-size:small; color:grey">(ACPD; DFNA68; HOMER-2; VESL-2; HOMER SCAFFOLD PROTEIN 2)</span><br>
+<li><a href="/showTopGene?topGene=EGR1">EGR1</a> <span style="font-size:small; color:grey">(AT225; G0S30; KROX-24; NGFI-A; TIS8; ZIF-268; ZNF225; EARLY GROWTH RESPONSE 1)</span><br>
+<li><a href="/showTopGene?topGene=ACHE">ACHE</a> <span style="font-size:small; color:grey">(ACEE; ARACHE; N-ACHE; ACETYLCHOLINESTERASE CARTWRIGHT BLOOD GROUP)</span><br>
+<li><a href="/showTopGene?topGene=NKS1">NKS1</a> <span style="font-size:small; color:grey">('EC-1; NATURAL KILLER CELL SUSCEPTIBILITY 1)</span><br>
+<li><a href="/showTopGene?topGene=GNRH1">GNRH1</a> <span style="font-size:small; color:grey">(GNRH; LHRH; LNRH; GONADOTROPIN RELEASING HORMONE 1)</span><br>
+<li><a href="/showTopGene?topGene=EGF">EGF</a> <span style="font-size:small; color:grey">(HOMG4; EPIDERMAL GROWTH FACTOR)</span><br>
+<li><a href="/showTopGene?topGene=CRHR2">CRHR2</a> <span style="font-size:small; color:grey">(CRF-RB; CRF2; CRFR2; HM-CRF; CORTICOTROPIN RELEASING HORMONE RECEPTOR 2)</span><br>
+<li><a href="/showTopGene?topGene=TAAR1">TAAR1</a> <span style="font-size:small; color:grey">(TAR1; TRAR1; TRACE AMINE ASSOCIATED RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=ADA">ADA</a> <span style="font-size:small; color:grey">(ADENOSINE DEAMINASE)</span><br>
+<li><a href="/showTopGene?topGene=MECP2">MECP2</a> <span style="font-size:small; color:grey">(AUTSX3; MRX16; MRX79; MRXS13; MRXSL; PPMX; METHYL-CPG BINDING PROTEIN 2)</span><br>
+<li><a href="/showTopGene?topGene=APOE">APOE</a> <span style="font-size:small; color:grey">(APO-E; APOE4; LDLCQ5; APOLIPOPROTEIN E)</span><br>
+<li><a href="/showTopGene?topGene=NFKB1">NFKB1</a> <span style="font-size:small; color:grey">(CVID12; EBP-1; KBF1; NF-KB1; NF-KAPPA-B1; NF-KAPPAB; NFKB-P105; NFKB-P50; NFKAPPAB; NUCLEAR FACTOR KAPPA B SUBUNIT 1)</span><br>
+<li><a href="/showTopGene?topGene=TPH2">TPH2</a> <span style="font-size:small; color:grey">(ADHD7; NTPH; TRYPTOPHAN HYDROXYLASE 2)</span><br>
+<li><a href="/showTopGene?topGene=PRKAB1">PRKAB1</a> <span style="font-size:small; color:grey">(AMPK; HAMPKB; PROTEIN KINASE AMP-ACTIVATED NON-CATALYTIC SUBUNIT BETA 1)</span><br>
+<li><a href="/showTopGene?topGene=PRKAA2">PRKAA2</a> <span style="font-size:small; color:grey">(AMPK; AMPK2; AMPKA2; PRKAA; PROTEIN KINASE AMP-ACTIVATED CATALYTIC SUBUNIT ALPHA 2)</span><br>
+<li><a href="/showTopGene?topGene=PRKAA1">PRKAA1</a> <span style="font-size:small; color:grey">(AMPK; AMPKA1; PROTEIN KINASE AMP-ACTIVATED CATALYTIC SUBUNIT ALPHA 1)</span><br>
+<li><a href="/showTopGene?topGene=MMP9">MMP9</a> <span style="font-size:small; color:grey">(CLG4B; GELB; MANDP2; MMP-9; MATRIX METALLOPEPTIDASE 9)</span><br>
+<li><a href="/showTopGene?topGene=ADH7">ADH7</a> <span style="font-size:small; color:grey">(ADH4; ALCOHOL DEHYDROGENASE 7 CLASS IV , MU OR SIGMA POLYPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=MPO">MPO</a> <span style="font-size:small; color:grey">(MYELOPEROXIDASE)</span><br>
+<li><a href="/showTopGene?topGene=VEGFA">VEGFA</a> <span style="font-size:small; color:grey">(MVCD1; VEGF; VASCULAR ENDOTHELIAL GROWTH FACTOR A)</span><br>
+<li><a href="/showTopGene?topGene=HCRT">HCRT</a> <span style="font-size:small; color:grey">(NRCLP1; PPOX; HYPOCRETIN NEUROPEPTIDE PRECURSOR)</span><br>
+<li><a href="/showTopGene?topGene=CYP1A1">CYP1A1</a> <span style="font-size:small; color:grey">(AHRR; CP11; CYP1; CYPIA1; P1-450; P450-C; P450DX; CYTOCHROME P450 FAMILY 1 SUBFAMILY A MEMBER 1)</span><br>
+<li><a href="/showTopGene?topGene=CHRNB3">CHRNB3</a> <span style="font-size:small; color:grey">(CHOLINERGIC RECEPTOR NICOTINIC BETA 3 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=CHRNB2">CHRNB2</a> <span style="font-size:small; color:grey">(EFNL3; NACHRB2; CHOLINERGIC RECEPTOR NICOTINIC BETA 2 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=VIP">VIP</a> <span style="font-size:small; color:grey">(PHM27; VASOACTIVE INTESTINAL PEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=TACR1">TACR1</a> <span style="font-size:small; color:grey">(NK1R; NKIR; TAC1R; TACHYKININ RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=RGS9">RGS9</a> <span style="font-size:small; color:grey">(PERRS; RGS9L; REGULATOR OF G PROTEIN SIGNALING 9)</span><br>
+<li><a href="/showTopGene?topGene=NR4A2">NR4A2</a> <span style="font-size:small; color:grey">(HZF-3; NURR1; RNR1; TINUR; NUCLEAR RECEPTOR SUBFAMILY 4 GROUP A MEMBER 2)</span><br>
+<li><a href="/showTopGene?topGene=HCRTR2">HCRTR2</a> <span style="font-size:small; color:grey">(OX2R; HYPOCRETIN RECEPTOR 2)</span><br>
+<li><a href="/showTopGene?topGene=GRM3">GRM3</a> <span style="font-size:small; color:grey">(GLUR3; GPRC1C; MGLUR3; MGLU3; GLUTAMATE METABOTROPIC RECEPTOR 3)</span><br>
+<li><a href="/showTopGene?topGene=CYP1A2">CYP1A2</a> <span style="font-size:small; color:grey">(CP12; CYPIA2; P3-450; P450 PA ; CYTOCHROME P450 FAMILY 1 SUBFAMILY A MEMBER 2)</span><br>
+<li><a href="/showTopGene?topGene=AP5B1">AP5B1</a> <span style="font-size:small; color:grey">(AP-5; PP1030; ADAPTOR RELATED PROTEIN COMPLEX 5 SUBUNIT BETA 1)</span><br>
+<li><a href="/showTopGene?topGene=PRKCG">PRKCG</a> <span style="font-size:small; color:grey">(PKC-GAMMA; PKCC; PKCG; PKCI 3 ; PKCGAMMA; SCA14; PROTEIN KINASE C GAMMA)</span><br>
+<li><a href="/showTopGene?topGene=SIRT1">SIRT1</a> <span style="font-size:small; color:grey">(SIR2; SIR2L1; SIR2ALPHA; SIRTUIN 1)</span><br>
+<li><a href="/showTopGene?topGene=RGS4">RGS4</a> <span style="font-size:small; color:grey">(RGP4; SCZD9; REGULATOR OF G PROTEIN SIGNALING 4)</span><br>
+<li><a href="/showTopGene?topGene=PTH">PTH</a> <span style="font-size:small; color:grey">(PTH1; PARATHYROID HORMONE)</span><br>
+<li><a href="/showTopGene?topGene=PER2">PER2</a> <span style="font-size:small; color:grey">(FASPS; FASPS1; PERIOD CIRCADIAN REGULATOR 2)</span><br>
+<li><a href="/showTopGene?topGene=FGF2">FGF2</a> <span style="font-size:small; color:grey">(BFGF; FGF-2; FGFB; HBGF-2; FIBROBLAST GROWTH FACTOR 2)</span><br>
+<li><a href="/showTopGene?topGene=ADH1A">ADH1A</a> <span style="font-size:small; color:grey">(ADH1; ALCOHOL DEHYDROGENASE 1A CLASS I , ALPHA POLYPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=GRM7">GRM7</a> <span style="font-size:small; color:grey">(GLUR7; GPRC1G; MGLU7; MGLUR7; PPP1R87; GLUTAMATE METABOTROPIC RECEPTOR 7)</span><br>
+<li><a href="/showTopGene?topGene=ADH4">ADH4</a> <span style="font-size:small; color:grey">(ADH-2; HEL-S-4; ALCOHOL DEHYDROGENASE 4 CLASS II , PI POLYPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=NOS3">NOS3</a> <span style="font-size:small; color:grey">(ECNOS; ENOS; NITRIC OXIDE SYNTHASE 3)</span><br>
+<li><a href="/showTopGene?topGene=ITGAM">ITGAM</a> <span style="font-size:small; color:grey">(CD11B; CR3A; MAC-1; MAC1A; MO1A; SLEB6; INTEGRIN SUBUNIT ALPHA M)</span><br>
+<li><a href="/showTopGene?topGene=GSTM1">GSTM1</a> <span style="font-size:small; color:grey">(GST1; GSTM1-1; GSTM1A-1A; GSTM1B-1B; GTH4; GTM1; GLUTATHIONE S-TRANSFERASE MU 1)</span><br>
+<li><a href="/showTopGene?topGene=GPR55">GPR55</a> <span style="font-size:small; color:grey">(LPIR1; G PROTEIN-COUPLED RECEPTOR 55)</span><br>
+<li><a href="/showTopGene?topGene=CYP2C19">CYP2C19</a> <span style="font-size:small; color:grey">(CPCJ; CYP2C; CYPIIC17; CYPIIC19; P450C2C; P450IIC19; CYTOCHROME P450 FAMILY 2 SUBFAMILY C MEMBER 19)</span><br>
+<li><a href="/showTopGene?topGene=CCKBR">CCKBR</a> <span style="font-size:small; color:grey">('xxCCK-B; CCK2R; GASR; CHOLECYSTOKININ B RECEPTOR)</span><br>
+<li><a href="/showTopGene?topGene=TANK">TANK</a> <span style="font-size:small; color:grey">(I-TRAF; ITRAF; TRAF2; TRAF FAMILY MEMBER ASSOCIATED NFKB ACTIVATOR)</span><br>
+<li><a href="/showTopGene?topGene=NCAM1">NCAM1</a> <span style="font-size:small; color:grey">(CD56; MSK39; NCAM; NEURAL CELL ADHESION MOLECULE 1)</span><br>
+<li><a href="/showTopGene?topGene=KCNJ6">KCNJ6</a> <span style="font-size:small; color:grey">(BIR1; GIRK-2; GIRK2; KATP-2; KATP2; KCNJ7; KIR3.2; KPLBS; HIGIRK2; POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY J MEMBER 6)</span><br>
+<li><a href="/showTopGene?topGene=HMGB1">HMGB1</a> <span style="font-size:small; color:grey">(HMG-1; HMG1; HMG3; SBP-1; HIGH MOBILITY GROUP BOX 1)</span><br>
+<li><a href="/showTopGene?topGene=HDAC2">HDAC2</a> <span style="font-size:small; color:grey">(KDAC2; RPD3; YAF1; HISTONE DEACETYLASE 2)</span><br>
+<li><a href="/showTopGene?topGene=CHRM2">CHRM2</a> <span style="font-size:small; color:grey">(CHOLINERGIC RECEPTOR MUSCARINIC 2)</span><br>
+<li><a href="/showTopGene?topGene=CCL5">CCL5</a> <span style="font-size:small; color:grey">(D17S136E; RANTES; SCYA5; SIS-DELTA; SISD; TCP228; EOCP; C-C MOTIF CHEMOKINE LIGAND 5)</span><br>
+<li><a href="/showTopGene?topGene=ADCYAP1">ADCYAP1</a> <span style="font-size:small; color:grey">(PACAP; ADENYLATE CYCLASE ACTIVATING POLYPEPTIDE 1)</span><br>
+<li><a href="/showTopGene?topGene=SULT2A1">SULT2A1</a> <span style="font-size:small; color:grey">(DHEA-ST; DHEAS; ST2A1; ST2A3; HSTA; SULFOTRANSFERASE FAMILY 2A MEMBER 1)</span><br>
+<li><a href="/showTopGene?topGene=PER1">PER1</a> <span style="font-size:small; color:grey">(RIGUI; HPER; PERIOD CIRCADIAN REGULATOR 1)</span><br>
+<li><a href="/showTopGene?topGene=MMP2">MMP2</a> <span style="font-size:small; color:grey">(CLG4; CLG4A; MMP-2; MMP-II; MONA; TBE-1; MATRIX METALLOPEPTIDASE 2)</span><br>
+<li><a href="/showTopGene?topGene=ARRB2">ARRB2</a> <span style="font-size:small; color:grey">(ARB2; ARR2; BARR2; ARRESTIN BETA 2)</span><br>
+<li><a href="/showTopGene?topGene=AGRP">AGRP</a> <span style="font-size:small; color:grey">(AGRT; ASIP2; AGOUTI RELATED NEUROPEPTIDE)</span><br>
+<li><a href="/showTopGene?topGene=SOD2">SOD2</a> <span style="font-size:small; color:grey">(IPO-B; IPOB; MNSOD; MVCD6; MN-SOD; SUPEROXIDE DISMUTASE 2)</span><br>
+<li><a href="/showTopGene?topGene=MBP">MBP</a> <span style="font-size:small; color:grey">(MYELIN BASIC PROTEIN)</span><br>
+<li><a href="/showTopGene?topGene=GAD2">GAD2</a> <span style="font-size:small; color:grey">(GAD65; GLUTAMATE DECARBOXYLASE 2)</span><br>
+<li><a href="/showTopGene?topGene=EIF4EBP1">EIF4EBP1</a> <span style="font-size:small; color:grey">(4E-BP1; 4EBP1; BP-1; PHAS-I; EUKARYOTIC TRANSLATION INITIATION FACTOR 4E BINDING PROTEIN 1)</span><br>
+<li><a href="/showTopGene?topGene=CREM">CREM</a> <span style="font-size:small; color:grey">(CREM-2; ICER; HCREM-2; CAMP RESPONSIVE ELEMENT MODULATOR)</span><br>
+<li><a href="/showTopGene?topGene=CHRNA6">CHRNA6</a> <span style="font-size:small; color:grey">(CHNRA6; CHOLINERGIC RECEPTOR NICOTINIC ALPHA 6 SUBUNIT)</span><br>
+<li><a href="/showTopGene?topGene=ALK">ALK</a> <span style="font-size:small; color:grey">(CD246; NBLST3; ALK RECEPTOR TYROSINE KINASE)</span><br>
+<li><a href="/showTopGene?topGene=UGT2B7">UGT2B7</a> <span style="font-size:small; color:grey">(UDPGT 2B7; UDPGT 2B9; UDPGT2B7; UDPGTH2; UDPGTH-2; UGT2B9; UDP GLUCURONOSYLTRANSFERASE FAMILY 2 MEMBER B7)</span><br>
+<li><a href="/showTopGene?topGene=UGT1A4">UGT1A4</a> <span style="font-size:small; color:grey">(GNT1; HUG-BR2; UDPGT; UDPGT 1-4; UGT-1A; UGT-1D; UGT1; UGT1-01; UGT1-04; UGT1.1; UGT1.4; UGT1A; UGT1A1; UGT1A4S; UGT1D; HUG-BR1; UDP GLUCURONOSYLTRANSFERASE FAMILY 1 MEMBER A4)</span><br>
+<li><a href="/showTopGene?topGene=SLC1A3">SLC1A3</a> <span style="font-size:small; color:grey">(EAAT1; GLAST; GLAST1; SOLUTE CARRIER FAMILY 1 MEMBER 3)</span><br>
+<li><a href="/showTopGene?topGene=SHBG">SHBG</a> <span style="font-size:small; color:grey">(TEBG; SEX HORMONE BINDING GLOBULIN)</span><br>
+<li><a href="/showTopGene?topGene=PARP1">PARP1</a> <span style="font-size:small; color:grey">(ADPRT; ADPRT 1; ADPRT1; ARTD1; PARP; PARP-1; PPOL; PADPRT-1; POLY ADP-RIBOSE POLYMERASE 1)</span><br>
+<li><a href="/showTopGene?topGene=NLRP3">NLRP3</a> <span style="font-size:small; color:grey">(AGTAVPRL; C1ORF7; CIAS1; CLR1.1; DFNA34; FCAS; FCAS1; KEFH; NALP3; PYPAF1; NLR FAMILY PYRIN DOMAIN CONTAINING 3)</span><br>
+<li><a href="/showTopGene?topGene=NFE2L2">NFE2L2</a> <span style="font-size:small; color:grey">(HEBP1; IMDDHH; NRF2; NUCLEAR FACTOR, ERYTHROID 2 LIKE 2)</span><br>
+<li><a href="/showTopGene?topGene=IL1RN">IL1RN</a> <span style="font-size:small; color:grey">(DIRA; ICIL-1RA; IL-1RN; IL-1RA; IL-1RA3; IL1F3; IL1RA; IRAP; MVCD4; INTERLEUKIN 1 RECEPTOR ANTAGONIST)</span><br>
+<li><a href="/showTopGene?topGene=GABPA">GABPA</a> <span style="font-size:small; color:grey">(E4TF1-60; E4TF1A; NFT2; NRF2; NRF2A; RCH04A07; GA BINDING PROTEIN TRANSCRIPTION FACTOR SUBUNIT ALPHA)</span><br>
+<li><a href="/showTopGene?topGene=FKBP5">FKBP5</a> <span style="font-size:small; color:grey">(AIG6; FKBP51; FKBP54; PPIASE; PTG-10; FKBP PROLYL ISOMERASE 5)</span><br>
+<li><a href="/showTopGene?topGene=ALDH1A1">ALDH1A1</a> <span style="font-size:small; color:grey">(ALDC; ALDH-E1; ALDH1; ALDH11; HEL-9; HEL-S-53E; HEL12; PUMB1; RALDH1; ALDEHYDE DEHYDROGENASE 1 FAMILY MEMBER A1)</span><br>
+<li><a href="/showTopGene?topGene=UGT1A6">UGT1A6</a> <span style="font-size:small; color:grey">(GNT1; HLUGP; HLUGP1; UDPGT; UDPGT 1-6; UGT-1A; UGT-1C; UGT-1E; UGT1; UGT1-01; UGT1-03; UGT1-05; UGT1.1; UGT1.3; UGT1.5; UGT1A; UGT1A1; UGT1A3; UGT1A5; UGT1A6S; UGT1C; UGT1E; UGT1F; HUG-BR1; UDP GLUCURONOSYLTRANSFERASE FAMILY 1 MEMBER A6)</span><br>
+<li><a href="/showTopGene?topGene=SIGMAR1">SIGMAR1</a> <span style="font-size:small; color:grey">(ALS16; DSMA2; OPRS1; SIG-1R; SR-BP; SR-BP1; SRBP; HSIGMAR1; SIGMA1R; SIGMA NON-OPIOID INTRACELLULAR RECEPTOR 1)</span><br>
+<li><a href="/showTopGene?topGene=RAC1">RAC1</a> <span style="font-size:small; color:grey">(MIG5; MRD48; RAC-1; TC-25; P21-RAC1; RAC FAMILY SMALL GTPASE 1)</span><br>
+<li><a href="/showTopGene?topGene=P4HTM">P4HTM</a> <span style="font-size:small; color:grey">(EGLN4; HIFPH4; P4H-TM; 'PH-4; PHD4; PROLYL 4-HYDROXYLASE, TRANSMEMBRANE)</span><br>
+<li><a href="/showTopGene?topGene=KRAS">KRAS</a> <span style="font-size:small; color:grey">(C-K-RAS; CFC2; K-RAS2A; K-RAS2B; K-RAS4A; K-RAS4B; K-RAS; KI-RAS; KRAS1; KRAS2; RALD; RASK2; C-KI-RAS2; KRAS PROTO-ONCOGENE, GTPASE)</span><br>
+<li><a href="/showTopGene?topGene=IL18">IL18</a> <span style="font-size:small; color:grey">(IGIF; IL-18; IL-1G; IL1F4; INTERLEUKIN 18)</span><br>
+<li><a href="/showTopGene?topGene=HTR3A">HTR3A</a> <span style="font-size:small; color:grey">(5-HT-3; 5-HT3A; 5-HT3R; 5HT3R; HTR3; 5-HYDROXYTRYPTAMINE RECEPTOR 3A)</span><br>
+<li><a href="/showTopGene?topGene=HSPA4">HSPA4</a> <span style="font-size:small; color:grey">(APG-2; HEL-S-5A; HS24/P52; HSPH2; HSP70; HSP70RY; HEAT SHOCK PROTEIN FAMILY A HSP70 MEMBER 4)</span><br>
+<li><a href="/showTopGene?topGene=FYN">FYN</a> <span style="font-size:small; color:grey">(P59-FYN; FYN PROTO-ONCOGENE, SRC FAMILY TYROSINE KINASE)</span><br>
+<li><a href="/showTopGene?topGene=COL11A2">COL11A2</a> <span style="font-size:small; color:grey">(DFNA13; DFNB53; FBCG2; HKE5; OSMEDA; OSMEDB; PARP; STL3; COLLAGEN TYPE XI ALPHA 2 CHAIN)</span><br>
+<li><a href="/showTopGene?topGene=UGT1A7">UGT1A7</a> <span style="font-size:small; color:grey">(GNT1; UDPGT; UDPGT 1-7; UGT-1A; UGT-1G; UGT1; UGT1-01; UGT1-07; UGT1.1; UGT1.7; UGT1A; UGT1A1; UGT1G; HUG-BR1; UDP GLUCURONOSYLTRANSFERASE FAMILY 1 MEMBER A7)</span><br>
+<li><a href="/showTopGene?topGene=TRPA1">TRPA1</a> <span style="font-size:small; color:grey">(ANKTM1; FEPS; FEPS1; TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL SUBFAMILY A MEMBER 1)</span><br>
+<li><a href="/showTopGene?topGene=STAT3">STAT3</a> <span style="font-size:small; color:grey">(ADMIO; ADMIO1; APRF; HIES; SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3)</span><br>
+<li><a href="/showTopGene?topGene=PRKCA">PRKCA</a> <span style="font-size:small; color:grey">(AAG6; PKC-ALPHA; PKCA; PKCI+/-; PKCALPHA; PRKACA; PROTEIN KINASE C ALPHA)</span><br>
+<li><a href="/showTopGene?topGene=MTHFR">MTHFR</a> <span style="font-size:small; color:grey">(METHYLENETETRAHYDROFOLATE REDUCTASE)</span><br>
+<li><a href="/showTopGene?topGene=GRK2">GRK2</a> <span style="font-size:small; color:grey">(ADRBK1; BARK1; BETA-ARK1; G PROTEIN-COUPLED RECEPTOR KINASE 2)</span><br>
+<li><a href="/showTopGene?topGene=DNMT1">DNMT1</a> <span style="font-size:small; color:grey">(ADCADN; CXXC9; DNMT; HSN1E; MCMT; M.HSAI; DNA METHYLTRANSFERASE 1)</span><br>
+<li><a href="/showTopGene?topGene=UGT1A8">UGT1A8</a> <span style="font-size:small; color:grey">(GNT1; UDPGT; UDPGT 1-8; UGT-1A; UGT-1H; UGT1; UGT1-01; UGT1-08; UGT1.1; UGT1.8; UGT1A; UGT1A1; UGT1A8S; UGT1H; HUG-BR1; UDP GLUCURONOSYLTRANSFERASE FAMILY 1 MEMBER A8)</span><br>
-<li><a href="/showTopGene?topGene=FOS">FOS</a><br>
-<li><a href="/showTopGene?topGene=BDNF">BDNF</a><br>
-<li><a href="/showTopGene?topGene=DRD2">DRD2</a><br>
-<li><a href="/showTopGene?topGene=OPRM1">OPRM1</a><br>
-<li><a href="/showTopGene?topGene=TH">TH</a><br>
-<li><a href="/showTopGene?topGene=ALDH2">ALDH2</a><br>
-<li><a href="/showTopGene?topGene=TNF">TNF</a><br>
-<li><a href="/showTopGene?topGene=CHRNA5">CHRNA5</a><br>
-<li><a href="/showTopGene?topGene=NPY">NPY</a><br>
-<li><a href="/showTopGene?topGene=FAAH">FAAH</a><br>
-<li><a href="/showTopGene?topGene=CCK">CCK</a><br>
-<li><a href="/showTopGene?topGene=COMT">COMT</a><br>
-<li><a href="/showTopGene?topGene=CYP2A6">CYP2A6</a><br>
-<li><a href="/showTopGene?topGene=DRD4">DRD4</a><br>
-<li><a href="/showTopGene?topGene=ARC">ARC</a><br>
-<li><a href="/showTopGene?topGene=CHRNA3">CHRNA3</a><br>
-<li><a href="/showTopGene?topGene=FOSB">FOSB</a><br>
-<li><a href="/showTopGene?topGene=CRH">CRH</a><br>
-<li><a href="/showTopGene?topGene=TLR4">TLR4</a><br>
-<li><a href="/showTopGene?topGene=TAT">TAT</a><br>
-<li><a href="/showTopGene?topGene=APP">APP</a><br>
-<li><a href="/showTopGene?topGene=TRPV1">TRPV1</a><br>
-<li><a href="/showTopGene?topGene=GABRA2">GABRA2</a><br>
-<li><a href="/showTopGene?topGene=CYP2E1">CYP2E1</a><br>
-<li><a href="/showTopGene?topGene=CYP2D6">CYP2D6</a><br>
-<li><a href="/showTopGene?topGene=ANKK1">ANKK1</a><br>
-<li><a href="/showTopGene?topGene=CORT">CORT</a><br>
-<li><a href="/showTopGene?topGene=PDYN">PDYN</a><br>
-<li><a href="/showTopGene?topGene=POMC">POMC</a><br>
-<li><a href="/showTopGene?topGene=CNR1">CNR1</a><br>
-<li><a href="/showTopGene?topGene=CNR1">CNR1</a><br>
-<li><a href="/showTopGene?topGene=CHRNB4">CHRNB4</a><br>
-<li><a href="/showTopGene?topGene=SLC6A3">SLC6A3</a><br>
-<li><a href="/showTopGene?topGene=HTT">HTT</a><br>
-<li><a href="/showTopGene?topGene=JUN">JUN</a><br>
-<li><a href="/showTopGene?topGene=NGF">NGF</a><br>
-<li><a href="/showTopGene?topGene=GDNF">GDNF</a><br>
-<li><a href="/showTopGene?topGene=DBH">DBH</a><br>
-<li><a href="/showTopGene?topGene=GFAP">GFAP</a><br>
-<li><a href="/showTopGene?topGene=AVP">AVP</a><br>
-<li><a href="/showTopGene?topGene=MTOR">MTOR</a><br>
-<li><a href="/showTopGene?topGene=DRD3">DRD3</a><br>
-<li><a href="/showTopGene?topGene=SLC6A4">SLC6A4</a><br>
-<li><a href="/showTopGene?topGene=MAOA">MAOA</a><br>
-<li><a href="/showTopGene?topGene=CYP2B6">CYP2B6</a><br>
-<li><a href="/showTopGene?topGene=TRH">TRH</a><br>
-<li><a href="/showTopGene?topGene=OPRK1">OPRK1</a><br>
-<li><a href="/showTopGene?topGene=DRD1">DRD1</a><br>
-<li><a href="/showTopGene?topGene=OPRD1">OPRD1</a><br>
-<li><a href="/showTopGene?topGene=CDK5">CDK5</a><br>
-<li><a href="/showTopGene?topGene=BCHE">BCHE</a><br>
-<li><a href="/showTopGene?topGene=CRP">CRP</a><br>
-<li><a href="/showTopGene?topGene=BAX">BAX</a><br>
-<li><a href="/showTopGene?topGene=PENK">PENK</a><br>
-<li><a href="/showTopGene?topGene=CHRNA4">CHRNA4</a><br>
-<li><a href="/showTopGene?topGene=CHAT">CHAT</a><br>
-<li><a href="/showTopGene?topGene=NPFF">NPFF</a><br>
-<li><a href="/showTopGene?topGene=SRC">SRC</a><br>
-<li><a href="/showTopGene?topGene=CYP3A4">CYP3A4</a><br>
-<li><a href="/showTopGene?topGene=ABCB1">ABCB1</a><br>
-<li><a href="/showTopGene?topGene=MECP2">MECP2</a><br>
-<li><a href="/showTopGene?topGene=HOMER2">HOMER2</a><br>
-<li><a href="/showTopGene?topGene=TAAR1">TAAR1</a><br>
-<li><a href="/showTopGene?topGene=EGFR">EGFR</a><br>
-<li><a href="/showTopGene?topGene=TPH2">TPH2</a><br>
-<li><a href="/showTopGene?topGene=HTR2A">HTR2A</a><br>
-<li><a href="/showTopGene?topGene=CCL2">CCL2</a><br>
-<li><a href="/showTopGene?topGene=OXT">OXT</a><br>
-<li><a href="/showTopGene?topGene=HCRT">HCRT</a><br>
-<li><a href="/showTopGene?topGene=CHRNB3">CHRNB3</a><br>
-<li><a href="/showTopGene?topGene=CHRNB2">CHRNB2</a><br>
-<li><a href="/showTopGene?topGene=RGS9">RGS9</a><br>
-<li><a href="/showTopGene?topGene=PER2">PER2</a><br>
-<li><a href="/showTopGene?topGene=CRHR1">CRHR1</a><br>
-<li><a href="/showTopGene?topGene=RGS4">RGS4</a><br>
-<li><a href="/showTopGene?topGene=MIF">MIF</a><br>
-<li><a href="/showTopGene?topGene=SIRT1">SIRT1</a><br>
-<li><a href="/showTopGene?topGene=DBI">DBI</a><br>
-<li><a href="/showTopGene?topGene=CHRM2">CHRM2</a><br>
-<li><a href="/showTopGene?topGene=MIP">MIP</a><br>
-<li><a href="/showTopGene?topGene=CCL4">CCL4</a><br>
-<li><a href="/showTopGene?topGene=APOE">APOE</a><br>
-<li><a href="/showTopGene?topGene=SNCA">SNCA</a><br>
-<li><a href="/showTopGene?topGene=PTH">PTH</a><br>
-<li><a href="/showTopGene?topGene=PER1">PER1</a><br>
-<li><a href="/showTopGene?topGene=GSTM1">GSTM1</a><br>
-<li><a href="/showTopGene?topGene=CHRNA6">CHRNA6</a><br>
-<li><a href="/showTopGene?topGene=HTR1B">HTR1B</a><br>
-<li><a href="/showTopGene?topGene=HMGB1">HMGB1</a><br>
-<li><a href="/showTopGene?topGene=ANG">ANG</a><br>
-<li><a href="/showTopGene?topGene=HDAC2">HDAC2</a><br>
-<li><a href="/showTopGene?topGene=GPR55">GPR55</a><br>
-<li><a href="/showTopGene?topGene=FYN">FYN</a><br>
-<li><a href="/showTopGene?topGene=AGRP">AGRP</a><br>
-<li><a href="/showTopGene?topGene=STAT3">STAT3</a><br>
-<li><a href="/showTopGene?topGene=MTHFR">MTHFR</a><br>
-<li><a href="/showTopGene?topGene=HOMER1">HOMER1</a><br>
-<li><a href="/showTopGene?topGene=GRIN1">GRIN1</a><br>
-<li><a href="/showTopGene?topGene=GAD1">GAD1</a><br>
-<li><a href="/showTopGene?topGene=GABRA1">GABRA1</a><br>
-<li><a href="/showTopGene?topGene=FKBP5">FKBP5</a><br>
-<li><a href="/showTopGene?topGene=EGR1">EGR1</a><br>
-<li><a href="/showTopGene?topGene=CYP2C19">CYP2C19</a><br>
-<li><a href="/showTopGene?topGene=VIP">VIP</a><br>
-<li><a href="/showTopGene?topGene=TRPA1">TRPA1</a><br>
-<li><a href="/showTopGene?topGene=NLRP3">NLRP3</a><br>
-<li><a href="/showTopGene?topGene=GRK2">GRK2</a><br>
-<li><a href="/showTopGene?topGene=GRIN2B">GRIN2B</a><br>
-<li><a href="/showTopGene?topGene=ARRB2">ARRB2</a><br>
-<li><a href="/showTopGene?topGene=ALDH1A1">ALDH1A1</a><br>
-<li><a href="/showTopGene?topGene=CYP1A2">CYP1A2</a><br>
-<li><a href="/showTopGene?topGene=CYP1A1">CYP1A1</a><br>
-<li><a href="/showTopGene?topGene=CNR2">CNR2</a><br>
-<li><a href="/showTopGene?topGene=MBP">MBP</a><br>
-<li><a href="/showTopGene?topGene=JUNB">JUNB</a><br>
-<li><a href="/showTopGene?topGene=GRIN2A">GRIN2A</a><br>
-<li><a href="/showTopGene?topGene=GRIA1">GRIA1</a><br>
-<li><a href="/showTopGene?topGene=FGF2">FGF2</a><br>
-<li><a href="/showTopGene?topGene=SP1">SP1</a><br>
-<li><a href="/showTopGene?topGene=NTRK2">NTRK2</a><br>
-<li><a href="/showTopGene?topGene=HTR3A">HTR3A</a><br>
-<li><a href="/showTopGene?topGene=OPRL1">OPRL1</a><br>
-<li><a href="/showTopGene?topGene=NR4A2">NR4A2</a><br>
-<li><a href="/showTopGene?topGene=EGF">EGF</a><br>
-<li><a href="/showTopGene?topGene=ALK">ALK</a><br>
-<li><a href="/showTopGene?topGene=NCAM1">NCAM1</a><br>
-<li><a href="/showTopGene?topGene=GAD2">GAD2</a><br>
-<li><a href="/showTopGene?topGene=CD14">CD14</a><br>
-<li><a href="/showTopGene?topGene=MAP2">MAP2</a><br>
-<li><a href="/showTopGene?topGene=HTR1A">HTR1A</a><br>
-<li><a href="/showTopGene?topGene=GRM3">GRM3</a><br>
-<li><a href="/showTopGene?topGene=CCL5">CCL5</a><br>
-<li><a href="/showTopGene?topGene=TACR1">TACR1</a><br>
-<li><a href="/showTopGene?topGene=NOS1">NOS1</a><br>
-<li><a href="/showTopGene?topGene=KCNJ6">KCNJ6</a><br>
-<li><a href="/showTopGene?topGene=HCRTR1">HCRTR1</a><br>
-<li><a href="/showTopGene?topGene=CREM">CREM</a><br>
-<li><a href="/showTopGene?topGene=CREB1">CREB1</a><br>
-<li><a href="/showTopGene?topGene=BCL2">BCL2</a><br>
-<li><a href="/showTopGene?topGene=SOD2">SOD2</a><br>
-<li><a href="/showTopGene?topGene=SNAP25">SNAP25</a><br>
-<li><a href="/showTopGene?topGene=DLG4">DLG4</a><br>
-<li><a href="/showTopGene?topGene=SLC18A2">SLC18A2</a><br>
-<li><a href="/showTopGene?topGene=MGLL">MGLL</a><br>
-<li><a href="/showTopGene?topGene=IL4">IL4</a><br>
-<li><a href="/showTopGene?topGene=IL1B">IL1B</a><br>
-<li><a href="/showTopGene?topGene=IL10">IL10</a><br>
-<li><a href="/showTopGene?topGene=GRM7">GRM7</a><br>
-<li><a href="/showTopGene?topGene=GRIA2">GRIA2</a><br>
-<li><a href="/showTopGene?topGene=DNMT1">DNMT1</a><br>
</ol>
-
{% endblock %}
diff --git a/extract_gene_symb_name_from_ncbi_gene_info.sh b/topGene_step0_extract_gene_alias_from_gene_info.sh
index 4d3118b..4d3118b 100644..100755
--- a/extract_gene_symb_name_from_ncbi_gene_info.sh
+++ b/topGene_step0_extract_gene_alias_from_gene_info.sh
diff --git a/topGene_step1_cnt_abstracts.py b/topGene_step1_cnt_abstracts.py
index a9dd23f..420c9cf 100755
--- a/topGene_step1_cnt_abstracts.py
+++ b/topGene_step1_cnt_abstracts.py
@@ -31,7 +31,6 @@ def saveStopWord(w):
swf.write(w+"\n")
return
-
# either start with ncbi_gene_symb_syno_name_txid9606 for fresh new counts
# or recount the results after adding additional stopwords
@@ -39,7 +38,6 @@ if len(sys.argv)==2:
input_f=sys.argv[1]
else:
input_f="./ncbi_gene_symb_syno_name_txid9606.txt"
- input_f="./ncbi_gene_symb_syno_name_txid9606_p2.txt"
addiction=undic(addiction_d)
drug=undic(drug_d)
@@ -53,50 +51,57 @@ with open (stopword_f, "r") as swf:
with open (input_f, "r") as f:
for line in f:
- rerun=0
- count=-1
+ do_search=0
inputline=line
+ line=line.replace("-","\ ")
+ # remove the annotated stopword
if "'" in line:
+ do_search=1
words=line.split("|")
line=str()
for word in words:
# ' is used to mark/annotate a word is a stop word in the results
+ # remove the ' mark
if "'" in word:
word=word.replace("'","")
stopWords.append(word)
saveStopWord(word)
- rerun=1
- # remove the ' mark
line+="|"+word
line=line[1:]
line=removeStopWords(line)
# tab is added if there are abstracts counts
if "\t" in line:
(gene, count)=line.split("\t")
- if int(count)<100:
- rerun=1
+ # rerun if count is low, these are less annotated
+ # if int(count)<50:
+ # do_search=1
else:
+ #no count,
gene=line.strip()
- # remove synonyms with only two letters
- if "|" in gene:
- synos=gene.split("|")
- gene=str()
- for syno in synos:
- if len(syno)>2:
- gene+="|"+syno
- gene=gene[1:]
- gene_q=gene.replace("|", "\"[tiab] OR \"")
- gene_q+="[tiab]"
- if rerun==1 or count== -1 :
+ do_search=1
+ if do_search==1:
+ # remove synonyms with only two letters
+ if "|" in gene:
+ synos=gene.split("|")
+ # keep the gene name regardless number of characters
+ gene=synos[0]
+ #print ("gene: "+gene + " synos -->" + str(synos[1:]))
+ for syno in synos[1:]:
+ #synonyms must be at least 3 characters
+ if len(syno)>3:
+ gene+="|"+syno
+ gene_q=gene.replace("|", "\"[tiab] OR \"")
+ gene_q+="[tiab]"
count=gene_addiction_cnt(gene_q)
- print("original line->\t"+inputline.strip())
- print("stopword rmed->\t"+line.strip())
- print("final result->\t"+gene+"\t"+count)
- # only save the non_zero results
- if (int(count)>0):
+ print("original line->\t"+inputline.strip())
+ print("stopword rmed->\t"+line.strip())
+ print("final result->\t"+gene+"\t"+count)
out.write(gene+"\t"+count)
+ else:
+ print("original resl->\t"+inputline.strip())
+ out.write(inputline)
-sorted_f=out_f.replace(".txt","_sorted.txt")
-os.system("sort -k2 -t$'\t' -rn " + out_f + " > " + sorted_f )
+sorted_f=output_f.replace(".txt","_sorted.txt")
+os.system("sort -k2 -t$'\t' -rn " + output_f + " > " + sorted_f )
diff --git a/topGene_step2_cnt_sentences.py b/topGene_step2_cnt_sentences.py
index fe97cdd..b05aa7a 100755
--- a/topGene_step2_cnt_sentences.py
+++ b/topGene_step2_cnt_sentences.py
@@ -1,5 +1,5 @@
#!/bin/env python3
-import os
+import os, sys
import re
import time
from nltk.tokenize import sent_tokenize
@@ -42,11 +42,18 @@ addiction=undic(addiction_d)
drug=undic(drug_d)
-out=open("gene_addiction_sentences.tab", "w+")
+out=open("topGene_addiction_sentences.tab", "w+")
cnt=0
-with open ("./ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted_absCnt_sorted.txt", "r") as f:
+
+if len(sys.argv) != 2:
+ print ("Please provide a sorted gene count file at the command line")
+ sys.exit()
+
+sorted_file=sys.argv[1] # ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted_absCnt_sorted_absCnt_sorted.txt
+with open (sorted_file, "r") as f:
for line in f:
(genes, abstractCount)=line.strip().split("\t")
+ genes=genes.replace("-","\ ")
if int(abstractCount)>20:
symb=genes.split("|")[0]
print(symb+"-->"+genes)
@@ -55,5 +62,4 @@ with open ("./ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted_absC
out.write(sentences)
out.close()
-os.system("cut -f 1,4 gene_addiction_sentences.tab |uniq |cut -f 1 |uniq -c |sort -rn > topGeneAbstractCount.tab")
-
+os.system("cut -f 1,4 topGene_addiction_sentences.tab |uniq |cut -f 1 |sort |uniq -c |sort -rn > topGeneAbstractCount.tab")
diff --git a/topGene_step3_generate_html.py b/topGene_step3_generate_html.py
index dfcd6fe..6755adb 100755
--- a/topGene_step3_generate_html.py
+++ b/topGene_step3_generate_html.py
@@ -1,14 +1,21 @@
import re
+import sys
## generate the html page for the top genes
## put gene names and alias in a dictionary
+#ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted_absCnt_absCnt_sorted.txt
+if (len(sys.argv) != 2):
+ print ("please provide the name of a sorted gene abstract count file")
+ sys.exit()
+
geneNames={}
-with open ("./ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted.txt","r") as f:
+with open (sys.argv[1],"r") as f:
for line in f:
(genes, count)=line.strip().split("\t")
gene=genes.split("|")
- geneNames[gene[0]]=genes.strip()
+ names=re.sub(r'^.*?\|', "", genes)
+ geneNames[gene[0]]=names.strip().replace("|", "; ")
out=str()
html=str()
@@ -20,8 +27,8 @@ with open("./topGeneAbstractCount.tab" ,"r") as gc:
print (line)
pmid_cnt, symb=line.strip().split()
out+= symb+"\t"+geneNames[symb]+"\n"
- html+="<li><a href=\"/showTopGene?topGene="+symb+"\">"+symb+"</a><br>\n"
- if cnt==500:
+ html+="<li><a href=\"/showTopGene?topGene="+symb+"\">"+symb+"</a> <span style=\"font-size:small; color:grey\">("+geneNames[symb]+")</span><br>\n"
+ if cnt==200:
break
with open("topGene_symb_alias.txt", "w+") as tg:
diff --git a/topGene_step4_get_pmids_for_all_top_genes.py b/topGene_step4_get_pmids_for_all_top_genes.py
new file mode 100755
index 0000000..9a18836
--- /dev/null
+++ b/topGene_step4_get_pmids_for_all_top_genes.py
@@ -0,0 +1,33 @@
+import os
+
+## save all pmids for the top genes so that I don't have to search for these.
+
+def getPMID(query):
+ print (query)
+ pmids=os.popen("esearch -db pubmed -query \"" + query + "\" | efetch -format uid").read()
+ return(pmids)
+
+def collectTerms():
+ pmids_f=open("topGene_all.pmid","w+")
+ with open("./topGene_symb_alias.txt", "r") as top:
+ q=str()
+ cnt=0
+ for one in top:
+ cnt+=1
+ (symb, alias)=one.split("\t")
+ q+="|"+alias.strip()
+ if (cnt==5):
+ print ("\n")
+ q=q[1:]
+ q=q.replace(";", "[tiab] OR ")+"[tiab]"
+ pmids=getPMID(q)
+ pmids_f.write(pmids)
+ cnt=0
+ q=str()
+ print("there should be nothing following the word empty"+q)
+
+collectTerms()
+os.system("sort topGene_all.pmid |uniq > topGene_uniq.pmid" )
+os.system("rm topGene_all.pmid")
+print ("results are in topGen_uniq.pmid")
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 00:29:19 +0000