Coexpression cluster:C600
From FANTOM5_SSTAR
Full id: C600_Reticulocytes_CD34_HES3GFP_Hep2_Mesenchymal_iPS_CD4
Phase1 CAGE Peaks
| Hg19::chr17:77429187..77429190,+ | p@chr17:77429187..77429190 + |
| Hg19::chr18:23751305..23751327,- | p1@ENST00000307796 |
| Hg19::chr1:120904659..120904667,+ | p1@ENST00000401004 |
| Hg19::chr1:120905986..120906002,+ | p1@HIST2H2BA |
| Hg19::chr1:149804218..149804222,+ | p11@HIST2H4A p11@HIST2H4B |
| Hg19::chr1:149812975..149812992,+ | p@chr1:149812975..149812992 + |
| Hg19::chr1:149822620..149822635,+ | p1@HIST2H2AA3 p1@HIST2H2AA4 |
| Hg19::chr1:149824160..149824183,+ | p1@HIST2H3A p1@HIST2H3C p1@HIST2H3D |
| Hg19::chr21:44985053..44985072,+ | p1@uc002zdj.1 |
| Hg19::chr22:51142547..51142550,- | p@chr22:51142547..51142550 - |
| Hg19::chr2:175366659..175366666,+ | p1@ENST00000313760 p1@ENST00000545980 |
| Hg19::chr6:27776055..27776066,+ | p19@HIST1H3H |
| Hg19::chr6:27791862..27791877,+ | p10@HIST1H4C p10@HIST1H4F p9@HIST1H4A p9@HIST1H4B p9@HIST1H4D p9@HIST1H4E p9@HIST1H4H p9@HIST1H4I p9@HIST1H4J p9@HIST1H4K p9@HIST1H4L p9@HIST2H4A p9@HIST2H4B p9@HIST4H4 |
| Hg19::chr6:32146268..32146280,+ | p2@RNF5 |
| Hg19::chrX:57301700..57301701,+ | p@chrX:57301700..57301701 + |
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:0000786 | nucleosome | 1.02889990100262e-05 |
| GO:0006334 | nucleosome assembly | 1.82795360157763e-05 |
| GO:0031497 | chromatin assembly | 1.82795360157763e-05 |
| GO:0006333 | chromatin assembly or disassembly | 2.69989057737589e-05 |
| GO:0065004 | protein-DNA complex assembly | 2.69989057737589e-05 |
| GO:0000785 | chromatin | 3.35101398552361e-05 |
| GO:0006325 | establishment and/or maintenance of chromatin architecture | 6.68254071514103e-05 |
| GO:0006323 | DNA packaging | 6.68254071514103e-05 |
| GO:0044427 | chromosomal part | 6.68254071514103e-05 |
| GO:0005694 | chromosome | 8.42194242363336e-05 |
| GO:0051276 | chromosome organization and biogenesis | 8.42194242363336e-05 |
| GO:0065003 | macromolecular complex assembly | 0.000215905675290121 |
| GO:0022607 | cellular component assembly | 0.000247612823251949 |
| GO:0006259 | DNA metabolic process | 0.000826583373718418 |
| GO:0006996 | organelle organization and biogenesis | 0.00139878014476753 |
| GO:0043234 | protein complex | 0.00791414839995249 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.00791414839995249 |
| GO:0043228 | non-membrane-bound organelle | 0.00791414839995249 |
| GO:0043283 | biopolymer metabolic process | 0.00941767443590979 |
| GO:0016043 | cellular component organization and biogenesis | 0.00998393556166264 |
| GO:0003677 | DNA binding | 0.0115816774323599 |
| GO:0032991 | macromolecular complex | 0.0148845201490435 |
| GO:0044446 | intracellular organelle part | 0.0163198533038729 |
| GO:0044422 | organelle part | 0.0163198533038729 |
| GO:0043170 | macromolecule metabolic process | 0.0277801155833588 |
| GO:0048015 | phosphoinositide-mediated signaling | 0.0348538768688054 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0394742815323511 |
| GO:0044237 | cellular metabolic process | 0.0398442130585918 |
| GO:0005634 | nucleus | 0.0398442130585918 |
| GO:0044238 | primary metabolic process | 0.0398442130585918 |
| GO:0003676 | nucleic acid binding | 0.0439843809381516 |
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><br>
| Ontology term | p-value | n |
|---|---|---|
| hematopoietic oligopotent progenitor cell | 2.61e-14 | 161 |
| hematopoietic multipotent progenitor cell | 2.61e-14 | 161 |
| hematopoietic stem cell | 1.36e-13 | 168 |
| angioblastic mesenchymal cell | 1.36e-13 | 168 |
| hematopoietic lineage restricted progenitor cell | 2.16e-13 | 120 |
| classical monocyte | 1.16e-12 | 42 |
| CD14-positive, CD16-negative classical monocyte | 1.16e-12 | 42 |
| myeloid cell | 1.21e-12 | 108 |
| common myeloid progenitor | 1.21e-12 | 108 |
| defensive cell | 4.03e-12 | 48 |
| phagocyte | 4.03e-12 | 48 |
| leukocyte | 5.29e-12 | 136 |
| hematopoietic cell | 7.47e-12 | 177 |
| myeloid lineage restricted progenitor cell | 4.07e-11 | 66 |
| granulocyte monocyte progenitor cell | 1.13e-10 | 67 |
| myeloid leukocyte | 1.17e-09 | 72 |
| macrophage dendritic cell progenitor | 4.24e-09 | 61 |
| nongranular leukocyte | 1.32e-08 | 115 |
| stuff accumulating cell | 2.83e-08 | 87 |
| monopoietic cell | 6.70e-08 | 59 |
| monocyte | 6.70e-08 | 59 |
| monoblast | 6.70e-08 | 59 |
| promonocyte | 6.70e-08 | 59 |
| Ontology term | p-value | n |
|---|---|---|
| larynx | 5.10e-12 | 9 |
| bone marrow | 2.00e-10 | 76 |
| skeletal element | 8.98e-10 | 90 |
| immune system | 1.87e-09 | 93 |
| bone element | 1.95e-09 | 82 |
| skeletal system | 3.91e-08 | 100 |
| upper respiratory tract | 9.09e-08 | 19 |
| hematopoietic system | 4.35e-07 | 98 |
| blood island | 4.35e-07 | 98 |
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) |
|---|---|
|
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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
No analysis results for this cluster
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.
