ENCODE ChIP-Seq Significance Tool

Instructions

YouTube Screencast

Change Log

(updated 04/13/2015)

Parameters

A Simple Web Tool to Identify Enriched ENCODE Transcription Factors

From a List of Genes or Transcripts



Funded in part by the March of Dimes Prematurity Research Center
Stanford University School of Medicine


Results

Organism

Select which organism to analyze.


Regulatory Element Type

Select whether to analyze protein-coding genes, protein-coding transcripts, pseudogenes, or pseudotranscripts (Annotation source: Gencode v15 [hg19]).

Feature Information

Select the type of identifiers used for your gene or transcript lists.
ID Type:

Gene List
One or more lists of genes (or transcripts, if selected above) to analyze. Identifiers must be of the type selected above. Multiple lists may be separated with "===" (please see Instructions link).

Enter Gene Symbols:
(one per line)
Example: HOXA1


Background Regions

A single list of genes (or transcripts) to use as the population for the hypergeometric test. Format is the same as the gene/transcript list above.

Default: Use all genes/transcripts that have the selected ID type.
All IDs   User List

Analysis Window Parameters

Select the point or region to use as the center of the analysis window.
Feature Type:

Select the size of the analysis window (in bp). Upstream and downstream distances are relative to the feature type selected above.
Upstream Pad:
Downstream Pad:

Cell Lines

The ENCODE cell lines to analyze. Selected cell lines are combined via union.

Default: Union of all available ENCODE cell lines. Please see the Cell Type Information link for detailed cell line descriptions.
All   Selected



Demonstrations

Clicking the buttons below will load sample data. Further information about each data set can be found via the Instructions link.

AAAYRNCTG Motif Example


Dexamethasone Example