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GeneProf database and analysis tool: GeneProf is a freely accessible, easy-to-use analysis environment for ChIP-seq and RNA-seq data and comes with a large database of ready-analysed public experiments, e.g. for transcription factor binding and histone modifications.
Central Motif Enrichment Analysis (CentriMo) is a tool for inferring direct DNA binding from ChIP-seq data. CentriMo is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. CentriMo takes a ...
ChIP has also been applied for genome-wide analysis by combining with microarray technology (ChIP-on-chip) or second-generation DNA-sequencing technology (Chip-Sequencing). ChIP can also combine with paired-end tags sequencing in Chromatin Interaction Analysis using Paired End Tag sequencing (ChIA-PET), a technique developed for large-scale, de ...
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
It is also possible to do more complex analysis using such tools like combining multiple ChIP-seq signal to detect regulatory sites. [10] In the context of ChIP-exo, this process is known as 'peak-pair calling'. [11] Differential peak calling is about identifying significant differences in two ChIP-seq signals. One can distinguish between one ...
GenePattern is a freely available online platform that provides access to RNA-Seq analysis methods without the need for programming. GeneProf Freely accessible, easy to use analysis pipelines for RNA-seq and ChIP-seq experiments. GREIN is an interactive web platform for re-processing and re-analyzing GEO RNA-seq data. GREIN is powered by the ...
ChIP-loop combines 3C with ChIP-seq to detect interactions between two loci of interest mediated by a protein of interest. [ 2 ] [ 46 ] The ChIP-loop may be useful in identifying long-range cis -interactions and trans interaction mediated through proteins since frequent DNA collisions will not occur.
Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points. [13]