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Factorbook specifications


Unique identifier OMICS_00533
Name Factorbook
Restrictions to use None
Maintained Yes


  • Primates
    • Homo sapiens

Publication for Factorbook

Factorbook citations


Widespread modulation of gene expression by copy number variation in skeletal muscle

Sci Rep
PMCID: 5780461
PMID: 29362391
DOI: 10.1038/s41598-018-19782-4

[…] V region by (i) mapping to the corresponding region in the human hg19 genome assembly using liftOver, (ii) counting the number of ChIP-seq experiments supporting binding of a TF according to ENCODE’s factorbook, and (iii) assessing statistical significance of the observed evidence as compared to 1000 randomly sampled genomic regions of the same size and chromosome using the regioneR package. CNV-a […]


THiCweed: fast, sensitive detection of sequence features by clustering big datasets

Nucleic Acids Res
PMCID: 5861420
PMID: 29267972
DOI: 10.1093/nar/gkx1251

[…] s that one considers; here we used 50 bp. We compare the discovered motifs to previously reported motifs from JASPAR (,); the THiCweed website also includes comparisons to motifs from HocoMoco () and FactorBook (). […]


Roles of alternative splicing in modulating transcriptional regulation

BMC Syst Biol
PMCID: 5629561
PMID: 28984199
DOI: 10.1186/s12918-017-0465-6

[…] ble S1). The splicing outcomes of these 165 exons are considered putative modulators.Fig. 2 In addition to RNA level datasets, the relationships between TFs and their targets were downloaded from the factorbook table, disseminated from the ENCODE database []. We focus our analysis on transcription factors and putative targets that with the expression samples over 400. This analysis obtained 226,02 […]


Genome wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer

PMCID: 5438707
PMID: 28423671
DOI: 10.18632/oncotarget.15993

[…] y using find individual motif occurrences (FIMO) with a p-value < 1e-4 to scan a +/− 100bp region around each probe using position weight matrices (PWMs) of human TF motif database JASPAR-Core [] and Factorbook []. Finally, ELMER determined the list of upstream regulatory TFs whose expression is associated with TF binding motif DNA methylation. For each motif, we calculated the average DNA methyla […]


Identification of Pathway Specific Serum Biomarkers of Response to Glucocorticoid and Infliximab Treatment in Children with Inflammatory Bowel Disease

PMCID: 5288595
PMID: 27628422
DOI: 10.1038/ctg.2016.49

[…] actor (NF)-κB or the glucocorticoid receptor (GR) steroidal transcription factor was examined using chromatin immunoprecipitation sequencing (ChIP-seq) data from ENCODE. ChIP-seq data from ENCODE and Factorbook was used to query physical binding of candidate gene promoters., Data/images were produced using UCSC Genome Browser Release 4 with alignment to human reference genome GRCh37/hg19., Withi […]


Identification of candidate genes for prostate cancer risk SNPs utilizing a normal prostate tissue eQTL data set

Nat Commun
PMCID: 4663677
PMID: 26611117
DOI: 10.1038/ncomms9653

[…] oised promoter, promoter, promoter+CTCF, insulator, enhancer, enhancer+CTCF, transcribed, repressed and heterochromatin).Bioinformatics tools used to map the regions of interest include FunciSNP (www.factorbook.org) and Regulome (http://regulome.stanford.edu/). By annotating SNPs with known and predicted regulatory elements, Regulome combines all of its sources to assign a causal score for a speci […]

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Factorbook institution(s)
Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA

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