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", Bioinformatics, 36(12):3902-3904, 2020). 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
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", Bioinformatics, 36(12):3902-3904, 2020). 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
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", Bioinformatics, 36(12):3902-3904, 2020). 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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