Coexpression cluster:C920
From FANTOM5_SSTAR
Full id: C920_anaplastic_adult_hereditary_cord_hairy_immature_xeroderma
Phase1 CAGE Peaks
| Hg19::chr17:53535935..53535939,+ | p@chr17:53535935..53535939 + |
| Hg19::chr17:80317121..80317128,+ | p1@TEX19 |
| Hg19::chr1:12123219..12123228,+ | p6@TNFRSF8 |
| Hg19::chr1:12123317..12123328,+ | p8@TNFRSF8 |
| Hg19::chr1:12123343..12123367,+ | p1@TNFRSF8 |
| Hg19::chr1:12123379..12123405,+ | p2@TNFRSF8 |
| Hg19::chr1:12123414..12123445,+ | p3@TNFRSF8 |
| Hg19::chr1:12124073..12124086,+ | p@chr1:12124073..12124086 + |
| Hg19::chr5:129083784..129083814,+ | p1@KIAA1024L |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
No results for this coexpression
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0045554 | regulation of TRAIL biosynthetic process | 0.000551925114800424 |
| GO:0032639 | TRAIL production | 0.000551925114800424 |
| GO:0045556 | positive regulation of TRAIL biosynthetic process | 0.000551925114800424 |
| GO:0045553 | TRAIL biosynthetic process | 0.000551925114800424 |
| GO:0042535 | positive regulation of tumor necrosis factor biosynthetic process | 0.00220770045920169 |
| GO:0042533 | tumor necrosis factor biosynthetic process | 0.00252308623908765 |
| GO:0042534 | regulation of tumor necrosis factor biosynthetic process | 0.00252308623908765 |
| GO:0032640 | tumor necrosis factor production | 0.00358751324620275 |
| GO:0042108 | positive regulation of cytokine biosynthetic process | 0.0100573020919188 |
| GO:0045727 | positive regulation of translation | 0.0103026021429412 |
| GO:0042035 | regulation of cytokine biosynthetic process | 0.0103026021429412 |
| GO:0031328 | positive regulation of cellular biosynthetic process | 0.0103026021429412 |
| GO:0042089 | cytokine biosynthetic process | 0.0103026021429412 |
| GO:0042107 | cytokine metabolic process | 0.0103026021429412 |
| GO:0009891 | positive regulation of biosynthetic process | 0.0103026021429412 |
| GO:0051247 | positive regulation of protein metabolic process | 0.011728408689509 |
| GO:0001816 | cytokine production | 0.0146747148170466 |
| GO:0006417 | regulation of translation | 0.0225676046940618 |
| GO:0031326 | regulation of cellular biosynthetic process | 0.0231227574411125 |
| GO:0009889 | regulation of biosynthetic process | 0.0236539334914467 |
| GO:0008285 | negative regulation of cell proliferation | 0.0236539334914467 |
| GO:0043065 | positive regulation of apoptosis | 0.0247646399336538 |
| GO:0043068 | positive regulation of programmed cell death | 0.0247646399336538 |
| GO:0031325 | positive regulation of cellular metabolic process | 0.0335754444836924 |
| GO:0009893 | positive regulation of metabolic process | 0.0345284351819145 |
| GO:0051246 | regulation of protein metabolic process | 0.035832676683966 |
| GO:0042127 | regulation of cell proliferation | 0.0383485746431702 |
| GO:0042981 | regulation of apoptosis | 0.0438494987758682 |
| GO:0043067 | regulation of programmed cell death | 0.0438494987758682 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| embryonic stem cell | 2.10e-18 | 5 |
| hematopoietic cell | 5.72e-13 | 177 |
| lymphoid lineage restricted progenitor cell | 1.46e-12 | 52 |
| lymphocyte | 2.94e-12 | 53 |
| common lymphoid progenitor | 2.94e-12 | 53 |
| nucleate cell | 1.10e-11 | 55 |
| hematopoietic oligopotent progenitor cell | 1.84e-11 | 161 |
| hematopoietic multipotent progenitor cell | 1.84e-11 | 161 |
| Langerhans cell | 2.08e-11 | 5 |
| lymphocyte of B lineage | 4.95e-11 | 24 |
| pro-B cell | 4.95e-11 | 24 |
| hematopoietic stem cell | 1.06e-10 | 168 |
| angioblastic mesenchymal cell | 1.06e-10 | 168 |
| germ line cell | 8.94e-09 | 7 |
| germ cell | 8.94e-09 | 7 |
| CD1a-positive Langerhans cell | 2.70e-08 | 2 |
| immature CD1a-positive Langerhans cell | 2.70e-08 | 2 |
| Ontology term | p-value | n |
|---|---|---|
| testis | 1.12e-07 | 8 |
| Ontology term | p-value | n |
|---|---|---|
| hematologic cancer | 4.46e-23 | 51 |
| immune system cancer | 4.46e-23 | 51 |
| lymphoma | 2.18e-13 | 10 |
| leukemia | 2.42e-12 | 39 |
| chronic leukemia | 1.02e-10 | 8 |
| myeloid leukemia | 1.65e-07 | 31 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| E2F6#1876 | 7 | 3.90223223576463 | 0.000306742359949273 | 0.00316278658611336 |
| EBF1#1879 | 6 | 5.93764456437934 | 0.000124243650792417 | 0.00165614328591056 |
| ELF1#1997 | 6 | 2.83873197253836 | 0.00720786312414863 | 0.0298592684472238 |
| JUND#3727 | 5 | 3.88592441215057 | 0.00454408927040116 | 0.0214810183909576 |
| MAFK#7975 | 6 | 18.0671554252199 | 1.92160575057211e-07 | 1.04744563144051e-05 |
| MAX#4149 | 6 | 4.30170367267141 | 0.000759756385172366 | 0.00596917152719602 |
| SIN3A#25942 | 5 | 3.00493595934174 | 0.0140161881734652 | 0.0491979793186979 |
| USF1#7391 | 5 | 3.53416626511553 | 0.0069229675408181 | 0.0293103537779918 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
