Supplementary Table 2. Overall results of WGCNA combined with differential expression between people with a history of alcohol use and controls BLA: basolateral amygdala
Authors:
Ponomarev I, Wang S, Zhang L, Harris RA, Mayfield RD
Genes that have enhancers which have changes in chromatin structure to state 4 or 5 in response to cocaine in adult (8-10 week) male C57BL/6J mice. 5hmC levels were measured via 5hmC-seq. Data taken from Supplementary Table 3. Values presented are "1" for presence. Data available at GEO with accession number GSE63749.
Differentially expressed genes in male Sprague-Dawley rats (300-375 g or 250-300 g) following cocaine administration. Gene expression was evaluated via RNA-seq. Data taken from Supplemental Table S1 (associated with Fig 2. E-F and H). Values presented are p-values. Data available at GEO with accession number GSE124055.
Authors:
Ashley E Lepack, Craig T Werner, Andrew F Stewart, Sasha L Fulton, Ping Zhong, Lorna A Farrelly, Alexander C W Smith, Aarthi Ramakrishnan, Yang Lyu, Ryan M Bastle, Jennifer A Martin, Swarup Mitra, Richard M O'Connor, Zi-Jun Wang, Henrik Molina, Gustavo Turecki, Li Shen, Zhen Yan, Erin S Calipari, David M Dietz, Paul J Kenny, Ian Maze
The total transcriptome including genes that are differentially expressed in cocaine addicts compared to control subjects. Post-mortem brain samples were collected from the dorsolateral prefrontal cortex (dlPFC) of the cocaine addict group and the control group. To assess gene expression, RNA-seq was performed. Data taken from Supplementary Table 2. Values presented are k.diff values. Data available from GEO with accession number GSE99349."
Authors:
Efrain A Ribeiro, Joseph R Scarpa, Susanna P Garamszegi, Andrew Kasarskis, Deborah C Mash, Eric J Nestler
Positional candidate genes for HOTPLATE_MEANOF2 in BXD RI Females on Chr11
Description:
Position candidates for HOTPLATE_MEANOF2 measured in BXD RI Females. HOTPLATE_MEANOF2 measures Thermal Nociception Hot Plate Avg of 2Trials under the domain Pain. The QTL found was a Significant QTL and spans 68 Mb to 70 Mb.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
F2 mice from a hybrid cross of C57BL/6J and FVB/NJ had heightened consumption of EtOH in 2 bottle, water versus ethanol, choice, with accending ethanol levels. Chromosome 11 had multiple suggestive markers, with LOD scores reflecting both additive and dominance variation taken together, as shown in Fig. 5.
Authors:
Phillips TJ, Reed C, Burkhart-Kasch S, Li N, Hitzemann R, Yu CH, Brown LL, Helms ML, Crabbe JC, Belknap JK
Heterozygote mice from a hybrid cross of C57BL/6J and FVB/NJ had heightened EtOH consumption, preference or blood EtOH concentration compared to either homozygous groups. The magnitude of dominant deviation on Chr. 11, as noted in Fig. 9, was measured after a drinking in the dark paradigm, 24hr two-bottle-choice and subsequent blood ethanol concentration measurement.
Authors:
Phillips TJ, Reed C, Burkhart-Kasch S, Li N, Hitzemann R, Yu CH, Brown LL, Helms ML, Crabbe JC, Belknap JK
QTL for chronic alcohol withdrawal severity on Chr11 at D11Mit4 (58.98 Mbp , Build 37)
Description:
chronic alcohol withdrawal severity spans 33.98 - 83.98 Mbp (NCBI Build 37) on Chr11. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
Bergeson SE, Kyle Warren R, Crabbe JC, Metten P, Gene Erwin V, Belknap JK
QTL for alcohol preference locus on Chr11 at NA (70.38 Mbp , Build 37)
Description:
alcohol preference locus spans 45.38 - 95.38 Mbp (NCBI Build 37) on Chr11. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for alcohol preference locus on Chr11 at D11Mit35 (80.34 Mbp , Build 37)
Description:
alcohol preference locus spans 55.34 - 105.34 Mbp (NCBI Build 37) on Chr11. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for nicotine sensitivity on Chr11 at D11Mit39 (81.17 Mbp , Build 37)
Description:
nicotine sensitivity spans 56.17 - 106.17 Mbp (NCBI Build 37) on Chr11. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Genes associated with Homo sapiens that interact with the MeSH term 'entinostat' (C118739). Incorporates data from 11 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'resveratrol' (C059514). Incorporates data from 16 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Bungarotoxins' (D002038). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'gamma-Aminobutyric Acid' (D005680). Incorporates data from 12 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Copper Sulfate' (D019327). Incorporates data from 72 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Electrophorus electricus that interact with the MeSH term 'Acetylcholine' (D000109). Incorporates data from 428 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Sarin' (D012524). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Oxygen' (D010100). Incorporates data from 8 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Muscimol' (D009118). Incorporates data from 3 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Plant Extracts' (D010936). Incorporates data from 489 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Vanadates' (D014638). Incorporates data from 150 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Cavia porcellus that interact with the MeSH term 'Ethanol' (D000431). Incorporates data from 17 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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