Maize Inflorescence
Toggle navigation
  • Information about Zea mays AGPv4. Click here for AGPv3
  • Home
  • About
      • About
      • Info
      • Team
      • Photos
      • Links
  • Outreach
  • Login
  • Convert AGPv3 AGPv4
  • Profile
    • Profile Display
    • Profile Search
    • Hierarchical Cluster
    • Heatmap
  • Sequence Analysis
    • Promoter Analysis
    • ChIP-seq Analysis
    • GO Term Restricted
    • BLAST search
    • SNP Annotation Restricted
    • Pathway analysis
  • Database
    • Interval Query
    • Gene list Query new
    • Gene Cluster
    • Keyword Search
    • Gene Network new
  • Genome Browser
  • MyGene Restricted
  • SNP in GWAS
  • SOP
  • Download
  • Outreach
  • Tutorial
  • Contact

ChIP-seq Peak Sequence Analysis

 Information

Given a list of gene ids, extract ChIP seq peak sequence within a defined window and run MAST program for motif scanning or run MEME program for motif discovery, with the database of motifs from JASPAR Core Plantae.
MEME-Suite: Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009. [full text]
JASPAR: Mathelier, A., Zhao, X., Zhang, A. W., Parcy, F., Worsley-Hunt, R., Arenillas, D. J., Buchman, S., Chen, C.-y., Chou, A., Ienasescu, H., Lim, J., Shyr, C., Tan, G., Zhou, M., Lenhard, B., Sandelin, A. and Wasserman, W. W. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research, 2013

 ChIP-seq peak sequence preparation

  • Extract the peak start and peak end position from the predicted peaks generated by MACS program.
  • Use the Maize genome FASTA file to retrieve the Peak sequence and store it in the database.

 Instructions

Steps to follow

  • Select the ChIP-seq experiments
  • Click on Example set of gene ids. to populate the box with example set of gene ids
    OR type in the desired list of gene ids in the box with one gene id per line.
  • Select the required length upstream of the genes, from the dropdown menu, wherein a motif peak has to be present.
  • Click on Get ChIP-seq Peaks
  • Wait for the page to load the ChIP peak sequences in tabular format, along with the peak name, peak position in the chromosome and peak summit.
  • Select the genes to do motif scanning or motif discovery. Perform motif scanning using MAST program in MEME Suite by clicking on Motif scanning using MAST
  • Wait for the appearance of a button MAST Output click this button to access the MAST results HTML page.
  • Select the genes to do motif scanning or motif discovery. Perform motif discovery using MEME program in MEME Suite by clicking on Motif discovery using MEME
  • Wait for the appearance of a button MEME Output click this button to access the MEME results HTML page.

Select the ChIP-seq experiments.





Gene ids list


Example set of gene ids.

Retrieve upstream

Sequences of length: