INsPeCT

Home
Flowcharts
User manual
Sample Datasets
About Us

ChIP-seq
Gene-list Analysis
Microarray
RMaNI
RNA-seq
WGCNA

ChIP-seq

Analysis name:

Please eneter a short name for your analysis

Data

Upload

Data file type:

Please select a filetype of your data.

Data file (zip):

Please upload zip file containing all the chip-seq data files of the filetype selected above.

Annotation file:

Please upload a sample annotation file. File must be in csv format with column headers. First column name must be sample names as in the data file and second column name must be "condition". Condition column format - "bgr1" or "sig1".

Perform quality control of the uploaded data. Report will be generated and saved in zip file.

GO enrichment analysis of the enriched peaks.

Extract enriched peak sequences.

Submit enriched peaks to MEME-ChIP.

Select upstream promoter region.

Select downstream promoter region.

Perform differential binding analysis. NOTE - This is only possible if you have replicates.

Differential gene expression analysis:

Gene-list Analysis Framework

Functional enrichmnent analysis using DAVID

Druggability analysis using CancerResource

Functional annotation of genes using gProfileR

Functional annotation of genes using EDanalysis

Gene Enrichment Disequilibrium Analysis using EDanalysis for BP

Gene Enrichment Disequilibrium Analysis using EDanalysis for MF

Gene Enrichment Disequilibrium Analysis using EDanalysis for CC

Promoter analysis

Select the upstream region:

Select the downstream region:

Extract the promoter sequences for the input genes

Detect CpG islands in the promoter sequences of the input genes

Remove sequences with over GC content in the promoter sequences of the input genes. (>55% GC content for human)

Submit the input genes to MEME Suite of tools for Motif Discovery, Motif Comparison and Motif Enrichment Analysis

Perform TFBS over-representation analysis using oPOSSUM

INsPeCT

Links

ChIP-seq