January 2018

The Human Epigenome Roadmap

Aside from the occasional somatic mutation, the genome of every cell in an individual’s body is largely preserved. Yet different types of cells (and tissues, and organs) are incredibly diverse. The majority of that specialization is governed by epigenetic changes — histone modifications, DNA accessibility, and methylation — that influence when and how genes are expressed.

Our knowledge of the epigenome has lagged well behind our knowledge of the genome, partly because it’s been difficult to study. The application of next-gen sequencing to RNA libraries (RNA-Seq),...

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MSigDB relate TFs to Genes

collection: Motif gene sets

Gene sets representing potential targets of regulation by transcription factors or microRNAs. The sets consist of genes grouped by short sequence motifs they share in their non-protein coding regions. The motifs represent known or likely cis-regulatory elements in promoters and 3'-UTRs. These gene sets make it possible to link changes in an expression profiling experiment to a putative cis-regulatory element. The C3 collection is divided into two sub-collections: microRNA targets (MIR) and transcription factor targets (TFT). 
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dbNSFP

Database type:          variant
Number of records:      89,617,785
Distinct variants:      84,484,850
Reference genome hg18:  chr, hg18_pos, ref, alt
Reference genome hg19:  chr, pos, ref, alt

Field:                  chr
Type:                   string
Comment:                Chromosome number
Missing entries:        0 
Unique Entries:         24

Field:                  pos
Type:                   integer
Comment:                physical position on the chromosome as to hg19
                        (1-based coordinate)
Missing entries:        0 
Unique Entries:         28,060,014
Range...
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