1. Pipelines
  2. ATAC-seq + ChIP-seq + DNase-seq

Activity by Contact

  • Status: active
Title
Activity by Contact
Assays
ATAC-seq, ChIP-seq, DNase-seq
Description
The Activity by Contact (ABC) model is designed to represent a mechanistic model in which enhancers activate gene transcription upon enhancer-promoter contact. In a simple conception of such a model, the quantitative effect of an enhancer depends on the frequency with which it contacts a promoter multiplied by the strength of the enhancer (i.e., the ability of the enhancer to activate transcription upon contacting a promoter). Moreover, the contribution of a specific enhancer to a gene’s expression should depend on the surrounding context (ie, the strength and contact frequency of other enhancers for the gene). To convert this conceptual framework into a practical score (which can be applied genome-wide), we formulated the ABC score: ABC score for effect of element E on gene G = Activity of E × Contact frequency between E and G / Sum of (Activity × Contact Frequency) over all candidate elements within 5 Mb. Operationally, Activity (A) is defined as the geometric mean of the read counts of DNase-seq and H3K27ac ChIP-seq at an element E, and Contact (C) as the KR normalized Hi-C contact frequency between E and the promoter of gene G. Elements are defined as ~500bp regions centered on DHS peaks. Note that the ABC model only considers candidate elements and genes on the same chromosome. It does not make interchromosomal predictions.
Lab
AMP-T2D consortium
Award PI
T2D AMP Consortium
Pipeline Type
github_readme
Workflow Language
python
Pipeline Output
predicted genes

Annotations

DSR510YWQ, DSR293FCZ, DSR255DSD, DSR262RCW, DSR777OUF, DSR031ZTG, DSR143KXJ, DSR109CTD, DSR804GYF, DSR273PHJ, DSR497YZL, DSR097EPN, DSR405NVR, DSR130JFC, DSR606LHI, DSR893IIE, DSR737ZLE, DSR739CIN, DSR823EJW, DSR553CQY, DSR815AUF, DSR700MOO, DSR091RQH, DSR868VDX, DSR371RIS, DSR199TJW, DSR612QOX, DSR128CAW, DSR094TTW, DSR139DEL, DSR982CMQ, DSR199UUA, DSR397ZRH, DSR645VYT, DSR708OVK, DSR886AVL, DSR485QCY, DSR233ZIX, DSR886XYE, DSR046SIQ, DSR549DHG, DSR132FCP, DSR015NPU, DSR694OVG, DSR599YMO, DSR784TGC, DSR327KAR, DSR876RQU, DSR252OJH, DSR627NNY, DSR319ZJZ, DSR506HNX, DSR734DGW, DSR117MIS, DSR932LQZ, DSR250DDG, DSR170XIW, DSR357IHY, DSR922GBW, DSR118KLN, DSR355NCA, DSR909VWD, DSR363VEB, DSR604IOP, DSR651DDS, DSR895REE, DSR384JYX, DSR544HLF, DSR028TMR, DSR670BGX, DSR412LFE, DSR093BCO, DSR926EGV, DSR232GSH, DSR494KQG, DSR379EHB, DSR249DLQ, DSR016HEL, DSR864GMH, DSR208GDM, DSR064TPU, DSR330HPF, DSR764OIT, DSR594LRQ, DSR598LAB, DSR666YAE, DSR069ZRF, DSR547QBE, DSR988OGT, DSR213AOJ, DSR988JBC, DSR831KJP, DSR593OAU, DSR284ZHE, DSR266GVV, DSR474NZP, DSR515WUM, DSR524YND, DSR619BAN, DSR821UNZ, DSR408DBU, DSR331JNK, DSR627FCC, DSR303OXY, DSR200CTI, DSR695DBX, DSR118ZZL, DSR632XJX, DSR692JFQ, DSR630TXR, DSR010MEO, DSR096TII, DSR254PVY, DSR719JYF, DSR769NVM, DSR781LHW, DSR503RPF, DSR117IFB, DSR406UXU, DSR987IVA, DSR344TRK, DSR507RTA, DSR120LQF, DSR083FZH, DSR797VJC, DSR155AOX, DSR563FIF, DSR486DHW, DSR154QOI, DSR695JEB, DSR770UIC, DSR941KCA, DSR542JXE, DSR164LWB, DSR039HOA, DSR328CUT, DSR715HCI, DSR633DNL, DSR051SJQ

Pipeline schematic

Documents

pipeline protocol
Description: ABC method
Attachment PDF Icon
ABC-method.pdf
Submitted by
Parul Kudtarkar
Lab
AMP-T2D consortium