Epigram

EPIPLAY: Clusters of motifs that interPLAY with the human EPIgenome

Presented here are clusters of motifs that interplay with the human epigenome. The motifs were identified by analyzing ChIP-Seq peaks of six core histone modifications and DNA methylation valleys (DMV) in human embryonic stem cells and four derived cell-types: human embryonic stem cells (H1), trophoblast-like (TBL), neural progenitor cell (NPC), mesendoderm (ME) and mesenchymal cells (MSC).

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Here we explain the layout of epiplay website.

Overview

2,034 de novo motifs that were found to be predictive of epigenomic modification and have Fisher’s exact test P-value < 1.0E-20 were clustered into 589 groups. The website provides an overview of: (i) the epigenomic modifications that the de novo interplay with, (ii) the cell-types in which the interplay occurs, (iii) the location preferences of the interplay, and (iv) the known motifs that match the de novo motifs.

Each motif group starts with a header that gives it's size and has a link to the tomtom results (matches to known motifs). Then each groups has between one and four tables:

Known motifs

This table details the known motifs that match the de novo motifs. It contains 11 columns:

  1. Symbol: the gene symbol of the known motif. In some cases when the known motif isn't human this is annotated in parentheses.
  2. Count: the number of de novo from that group that match the known motif.
  3. P-value: this is calculated using the hypergeometric distribution and represents how enriched the known motif is within the group. These are used for ranking the known motifs within the group.
  4. H1: the genes FPKM in H1 (the gene shown in the symbols column; expression values are only shown for human genes)
  5. ME: the genes FPKM in ME
  6. MSC: the genes FPKM in MSC
  7. NPC: the genes FPKM in NPC
  8. TBL: the genes FPKM in TBL
  9. Source DB the database that the known motif was taken from
  10. Interal ID the id that epiplay uses to represent the known motif
  11. Gene name the name of the gene (the gene shown in the symbols column; only shown if the symbol is present in humans)

Single mark analysis (Intra1)

This table details the de novo motifs in the group that were identified in the single mark analysis. It contains 13 columns:

  1. Internal ID: this is the internal ID that is assigned to the de novo motif
  2. Cell-type: this is the cell-type in which the de novo motif was found
  3. Mark: this is the epigenomic modification that in which the de novo motif was found
  4. ID: a second internal ID
  5. P-value: the Fisher’s exact test P-value that describes how enriched the de novo motif is within the ChIP-Seq peaks, in comparison to the background
  6. AUC: the area under the curve (AUC) that describes how enriched the de novo motif is within the ChIP-Seq peaks, in comparison to the background
  7. Pos class: there are three position classes which describe the motifs location preference within modification peaks: neutral, central and edge
  8. Pos P-value: the Chi-squared test P-value from the position analysis
  9. Bin 1 (edge): the weighted bin score used for the position class analysis
  10. Bin 2: the weighted bin score used for the position class analysis
  11. Bin 3: the weighted bin score used for the position class analysis
  12. Bin 4: the weighted bin score used for the position class analysis
  13. Bin 5 (middle): the weighted bin score used for the position class analysis

Mark specific analysis (Intra2)

This table details the de novo motifs in the group that were identified in the Mark specific analysis. It is in the same format as the Single mark analysis table.

Typical region background analysis (Intra3)

This table details the de novo motifs in the group that were identified in the Typical region background analysis. It is in the same format as the Single mark analysis table.

Cell-type specific analysis (Inter)

This table details the de novo motifs in the group that were identified in the Cell-type specific analysis. It is in the same format as the Single mark analysis table but with a few differences.

  1. Comparison: list the two cell-types that were being compared when the motif was identified
  2. Origin: list the cell-type in which the de novo motif is predictive of the modification