T-Gene Genomes and Tissue Panels

Genome + Histone/Expression Data

Human hg19 (ENCODE Tissue Panel)

Description: A panel of human histone modification and gene expression data from the ENCODE project. The tissues are the cell lines listed below (see also the paper on T-Gene: Timothy O'Connor, Charles E. Grant, Mikael Boden, Timothy L. Bailey, "T-Gene: Improved target gene prediction", bioRxiv, preprint, 2019). The type of RNA data used to measure expression levels is given below. The histone types used in the panel and the maximum link distance allowed for each histone type are listed below.

Genome Release: hg19

Annotation File: Panels/Human/Annotation/gencode.v7.transcripts.gtf

Tissues: Gm12878 H1hesc Helas3 Hepg2 Huvec K562 Nhek

Expression Data Type: Cage

Histone Modification(s): H3k27ac H3k4me3

Maximum Link Distance(s): 500000 1000

Low Expression Correlation Adjustment Threshold: 6.0

Human hg19 (Epigenomic Roadmap Tissue Panel)

Description: A panel of human histone modification and gene expression data from the Epigenetic Roadmap project (the 57 epigenome subset). The tissues are the cell lines whose IDs are listed below (see also the paper on T-Gene: Timothy O'Connor, Charles E. Grant, Mikael Boden, Timothy L. Bailey, "T-Gene: Improved target gene prediction", bioRxiv, preprint, 2019). The type of RNA data used to measure expression levels is given below. The histone type used in the panel and the maximum link distance allowed for each histone type are listed below.

Genome Release: hg19

Annotation File: Panels/Human/Annotation/gencode.v10.transcripts.gtf

Tissues: E003 E004 E005 E006 E007 E011 E012 E013 E016 E037 E038 E047 E050 E055 E056 E058 E059 E061 E062 E065 E066 E071 E079 E084 E085 E087 E094 E095 E096 E097 E098 E100 E104 E105 E106 E109 E112 E113 E114 E116 E117 E118 E119 E120 E122 E123 E127 E128

Expression Data Type: LongPap

Histone Modification(s): H3K27ac

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 6.0

Mouse mm9 (ENCODE Tissue Panel)

Description: A panel of mouse histone modification and gene expression data from the ENCODE project. The tissues are the listed below (see also the paper on T-Gene: Timothy O'Connor, Charles E. Grant, Mikael Boden, Timothy L. Bailey, "T-Gene: Improved target gene prediction", bioRxiv, preprint, 2019). The type of RNA data used to measure expression levels is given below. The histone types used in the panel and the maximum link distance allowed for each histone type are listed below.

Genome Release: mm9

Annotation File: Panels/Mouse/Annotation/mm9RefSeq.transcripts.named.gtf

Tissues: Bat_MAdult24wks Heart_MAdult8wks Lung_MAdult8wks Spleen_MAdult8wks Bmarrow_MAdult8wks Heart_UE14half Mef_MAdult8wks Testis_MAdult8wks Bmdm_FAdult8wks Kidney_MAdult8wks Mel_MImmortal Thymus_MAdult8wks Cbellum_MAdult8wks Limb_UE14half Olfact_MAdult8wks Wbrain_UE14half Cortex_MAdult8wks Liver_MAdult8wks Plac_FAdult8wks Esb4_ME0 Liver_UE14half Smint_MAdult8wks

Expression Data Type: LongPap

Histone Modification(s): H3k27ac H3k04me3

Maximum Link Distance(s): 500000 1000

Low Expression Correlation Adjustment Threshold: 6.0

Genomes Only

Arabidopsis thaliana TAIR10 (Ensembl)

Description: All transcripts in the Ensembl GTF file Arabidopsis_thaliana.TAIR10.44.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: TAIR10

Annotation File: Genomes/Arabidopsis_thaliana.TAIR10.44.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Caenorhabditis elegans WBcel235 (Ensembl)

Description: All transcripts in the Ensembl GTF file Caenorhabditis_elegans.WBcel235.44.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: WBcel235

Annotation File: Genomes/Caenorhabditis_elegans.WBcel235.44.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Caenorhabditis elegans ce11 (UCSC)

Description: All transcripts in the Ensembl GTF file Caenorhabditis_elegans.WBcel235.44.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: ce11

Annotation File: Genomes/Caenorhabditis_elegans.WBcel235.44.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Danio rerio GRCz11 (Ensembl)

Description: All transcripts in the Ensembl GTF file Danio_rerio.GRCz11.97.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: GRCz11

Annotation File: Genomes/Danio_rerio.GRCz11.97.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Danio rerio danRer11 (UCSC)

Description: All transcripts in the Ensembl GTF file Danio_rerio.GRCz11.97.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: danRer11

Annotation File: Genomes/Danio_rerio.GRCz11.97.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Drosophila melanogaster BDGP6 (Ensembl)

Description: All transcripts in the Ensembl GTF file Drosophila_melanogaster.BDGP6.22.44.chr.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: BDGP6

Annotation File: Genomes/Drosophila_melanogaster.BDGP6.22.44.chr.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Drosophila melanogaster dm6 (UCSC)

Description: All transcripts in the Ensembl GTF file Drosophila_melanogaster.BDGP6.22.44.chr.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: dm6

Annotation File: Genomes/Drosophila_melanogaster.BDGP6.22.44.chr.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Homo sapiens GRCh38 (Ensembl)

Description: All transcripts in the Ensembl GTF file Homo_sapiens.GRCh38.97.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: GRCh38

Annotation File: Genomes/Homo_sapiens.GRCh38.97.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Homo sapiens hg38 (UCSC)

Description: All transcripts in the Ensembl GTF file Homo_sapiens.GRCh38.97.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: hg38

Annotation File: Genomes/Homo_sapiens.GRCh38.97.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Mus musculus GRCm38 (Ensembl)

Description: All transcripts in the Ensembl GTF file Mus_musculus.GRCm38.97.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: GRCm38

Annotation File: Genomes/Mus_musculus.GRCm38.97.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Mus musculus mm10 (UCSC)

Description: All transcripts in the Ensembl GTF file Mus_musculus.GRCm38.97.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: mm10

Annotation File: Genomes/Mus_musculus.GRCm38.97.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Rattus norvegicus Rnor_6 (Ensembl)

Description: All transcripts in the Ensembl GTF file Rattus_norvegicus.Rnor_6.0.97.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: Rnor_6

Annotation File: Genomes/Rattus_norvegicus.Rnor_6.0.97.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Rattus norvegicus rn6 (UCSC)

Description: All transcripts in the Ensembl GTF file Rattus_norvegicus.Rnor_6.0.97.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: rn6

Annotation File: Genomes/Rattus_norvegicus.Rnor_6.0.97.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Saccharomyces cerevisiae R64-1-1 (Ensembl)

Description: All transcripts in the Ensembl GTF file Saccharomyces_cerevisiae.R64-1-1.97.gtf.gz. Chromosomes use the Ensembl nomenclature.

Genome Release: R64-1-1

Annotation File: Genomes/Saccharomyces_cerevisiae.R64-1-1.97.ensembl.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0

Saccharomyces cerevisiae sacCer3 (UCSC)

Description: All transcripts in the Ensembl GTF file Saccharomyces_cerevisiae.R64-1-1.97.gtf.gz. Chromosomes have been renamed to the UCSC nomenclature.

Genome Release: sacCer3

Annotation File: Genomes/Saccharomyces_cerevisiae.R64-1-1.97.ucsc.transcripts.gtf

Tissues: The tissues in the panel

Expression Data Type: none

Histone Modification(s): none

Maximum Link Distance(s): 500000

Low Expression Correlation Adjustment Threshold: 0.0