Coexpression cluster:C3704: Difference between revisions
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|full_id=C3704_Eosinophils_Basophils_Mast_CD14_mature_immature_Neutrophils
|id=C3704
}}") |
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{{Coexpression_clusters | 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tail shortening!0.00339482700640546!7538$GO:0017091!AU-rich element binding!0.00339482700640546!7538$GO:0050779!RNA destabilization!0.00339482700640546!7538$GO:0048731!system development!0.00339482700640546!7071;7538;81565$GO:0048856!anatomical structure development!0.00529648511130244!7071;7538;81565$GO:0007275!multicellular organismal development!0.00650898764464172!7071;7538;81565$GO:0000288!mRNA catabolic process, deadenylation-dependent decay!0.00650898764464172!7538$GO:0043487!regulation of RNA stability!0.00931831515612074!7538$GO:0043488!regulation of mRNA stability!0.00931831515612074!7538$GO:0031348!negative regulation of defense response!0.00931831515612074!7538$GO:0050728!negative regulation of inflammatory response!0.00931831515612074!7538$GO:0032502!developmental process!0.0102721473776894!7071;7538;81565$GO:0031124!mRNA 3'-end processing!0.0122633274630083!7538$GO:0032501!multicellular organismal process!0.0126504045457779!7071;7538;81565$GO:0045638!negative regulation of myeloid cell differentiation!0.0126504045457779!7538$GO:0031123!RNA 3'-end processing!0.0126504045457779!7538$GO:0051252!regulation of RNA metabolic process!0.0126504045457779!7538$GO:0003727!single-stranded RNA binding!0.0126504045457779!7538$GO:0031347!regulation of defense response!0.0142296101213018!7538$GO:0050727!regulation of inflammatory response!0.0142296101213018!7538$GO:0006402!mRNA catabolic process!0.0157184797707154!7538$GO:0045637!regulation of myeloid cell differentiation!0.016401392162261!7538$GO:0003729!mRNA binding!0.016401392162261!7538$GO:0048583!regulation of response to stimulus!0.016401392162261!7538$GO:0048523!negative regulation of cellular process!0.016401392162261!7071;7538$GO:0048513!organ development!0.016401392162261!7071;7538$GO:0048519!negative regulation of biological process!0.0169359510998705!7071;7538$GO:0006401!RNA catabolic process!0.0186902118941852!7538$GO:0007179!transforming growth factor beta receptor signaling pathway!0.0196126044726536!7071$GO:0045596!negative regulation of cell differentiation!0.0246356198112062!7538$GO:0007178!transmembrane receptor protein serine/threonine kinase signaling pathway!0.026074786722757!7071$GO:0030099!myeloid cell differentiation!0.026074786722757!7538$GO:0051093!negative regulation of developmental process!0.026074786722757!7538$GO:0005819!spindle!0.026074786722757!81565$GO:0048869!cellular developmental process!0.0294175409287247!7538;81565$GO:0030154!cell differentiation!0.0294175409287247!7538;81565$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0385264091806844!7071$GO:0005813!centrosome!0.0385264091806844!81565$GO:0045595!regulation of cell differentiation!0.0416849547241876!7538$GO:0005815!microtubule organizing center!0.0416849547241876!81565$GO:0030097!hemopoiesis!0.0445230348524182!7538$GO:0048534!hemopoietic or lymphoid organ development!0.0466859166721047!7538$GO:0002520!immune system 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| ||
|full_id=C3704_Eosinophils_Basophils_Mast_CD14_mature_immature_Neutrophils | |||
|id=C3704 | |||
}} | |||
Latest revision as of 12:31, 17 September 2013
Full id: C3704_Eosinophils_Basophils_Mast_CD14_mature_immature_Neutrophils
Phase1 CAGE Peaks
| Hg19::chr17:8339189..8339285,+ | p1@NDEL1 |
| Hg19::chr19:39897478..39897493,+ | p1@ZFP36 |
| Hg19::chr8:103667935..103667960,- | p1@KLF10 |
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:0000289 | poly(A) tail shortening | 0.00339482700640546 |
| GO:0017091 | AU-rich element binding | 0.00339482700640546 |
| GO:0050779 | RNA destabilization | 0.00339482700640546 |
| GO:0048731 | system development | 0.00339482700640546 |
| GO:0048856 | anatomical structure development | 0.00529648511130244 |
| GO:0007275 | multicellular organismal development | 0.00650898764464172 |
| GO:0000288 | mRNA catabolic process, deadenylation-dependent decay | 0.00650898764464172 |
| GO:0043487 | regulation of RNA stability | 0.00931831515612074 |
| GO:0043488 | regulation of mRNA stability | 0.00931831515612074 |
| GO:0031348 | negative regulation of defense response | 0.00931831515612074 |
| GO:0050728 | negative regulation of inflammatory response | 0.00931831515612074 |
| GO:0032502 | developmental process | 0.0102721473776894 |
| GO:0031124 | mRNA 3'-end processing | 0.0122633274630083 |
| GO:0032501 | multicellular organismal process | 0.0126504045457779 |
| GO:0045638 | negative regulation of myeloid cell differentiation | 0.0126504045457779 |
| GO:0031123 | RNA 3'-end processing | 0.0126504045457779 |
| GO:0051252 | regulation of RNA metabolic process | 0.0126504045457779 |
| GO:0003727 | single-stranded RNA binding | 0.0126504045457779 |
| GO:0031347 | regulation of defense response | 0.0142296101213018 |
| GO:0050727 | regulation of inflammatory response | 0.0142296101213018 |
| GO:0006402 | mRNA catabolic process | 0.0157184797707154 |
| GO:0045637 | regulation of myeloid cell differentiation | 0.016401392162261 |
| GO:0003729 | mRNA binding | 0.016401392162261 |
| GO:0048583 | regulation of response to stimulus | 0.016401392162261 |
| GO:0048523 | negative regulation of cellular process | 0.016401392162261 |
| GO:0048513 | organ development | 0.016401392162261 |
| GO:0048519 | negative regulation of biological process | 0.0169359510998705 |
| GO:0006401 | RNA catabolic process | 0.0186902118941852 |
| GO:0007179 | transforming growth factor beta receptor signaling pathway | 0.0196126044726536 |
| GO:0045596 | negative regulation of cell differentiation | 0.0246356198112062 |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | 0.026074786722757 |
| GO:0030099 | myeloid cell differentiation | 0.026074786722757 |
| GO:0051093 | negative regulation of developmental process | 0.026074786722757 |
| GO:0005819 | spindle | 0.026074786722757 |
| GO:0048869 | cellular developmental process | 0.0294175409287247 |
| GO:0030154 | cell differentiation | 0.0294175409287247 |
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.0385264091806844 |
| GO:0005813 | centrosome | 0.0385264091806844 |
| GO:0045595 | regulation of cell differentiation | 0.0416849547241876 |
| GO:0005815 | microtubule organizing center | 0.0416849547241876 |
| GO:0030097 | hemopoiesis | 0.0445230348524182 |
| GO:0048534 | hemopoietic or lymphoid organ development | 0.0466859166721047 |
| GO:0002520 | immune system development | 0.0479597324192457 |
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 |
|---|---|---|
| myeloid leukocyte | 1.09e-23 | 72 |
| classical monocyte | 2.73e-23 | 42 |
| CD14-positive, CD16-negative classical monocyte | 2.73e-23 | 42 |
| defensive cell | 1.85e-22 | 48 |
| phagocyte | 1.85e-22 | 48 |
| leukocyte | 2.31e-21 | 136 |
| granulocyte monocyte progenitor cell | 1.92e-20 | 67 |
| macrophage dendritic cell progenitor | 6.56e-18 | 61 |
| myeloid lineage restricted progenitor cell | 3.72e-17 | 66 |
| monopoietic cell | 8.67e-17 | 59 |
| monocyte | 8.67e-17 | 59 |
| monoblast | 8.67e-17 | 59 |
| promonocyte | 8.67e-17 | 59 |
| hematopoietic lineage restricted progenitor cell | 1.43e-14 | 120 |
| nongranular leukocyte | 1.12e-13 | 115 |
| stuff accumulating cell | 9.61e-09 | 87 |
| hematopoietic stem cell | 1.20e-08 | 168 |
| angioblastic mesenchymal cell | 1.20e-08 | 168 |
| myeloid cell | 7.66e-08 | 108 |
| common myeloid progenitor | 7.66e-08 | 108 |
| hematopoietic cell | 1.40e-07 | 177 |
| hematopoietic oligopotent progenitor cell | 1.78e-07 | 161 |
| hematopoietic multipotent progenitor cell | 1.78e-07 | 161 |
| Ontology term | p-value | n |
|---|---|---|
| hematopoietic system | 6.03e-20 | 98 |
| blood island | 6.03e-20 | 98 |
| bone marrow | 5.66e-19 | 76 |
| skeletal element | 3.90e-18 | 90 |
| hemolymphoid system | 5.57e-18 | 108 |
| bone element | 1.43e-17 | 82 |
| immune system | 1.96e-16 | 93 |
| skeletal system | 9.42e-16 | 100 |
| adult organism | 2.36e-09 | 114 |
| lateral plate mesoderm | 4.08e-09 | 203 |
| musculoskeletal system | 1.56e-07 | 167 |
| organ | 1.95e-07 | 503 |
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) |
|---|---|
| MA0003.1 | 3.8806 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 1.5435 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 3.90467 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 1.21731 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 0.658629 |
| MA0029.1 | 1.23771 |
| MA0030.1 | 1.22561 |
| MA0031.1 | 1.15713 |
| MA0038.1 | 0.94098 |
| MA0040.1 | 1.24388 |
| MA0041.1 | 0.847069 |
| MA0042.1 | 0.810843 |
| MA0043.1 | 1.32783 |
| MA0046.1 | 1.31611 |
| MA0048.1 | 0.341392 |
| MA0050.1 | 0.81185 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 0.190716 |
| MA0056.1 | 0 |
| MA0057.1 | 0.886807 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 1.23283 |
| MA0061.1 | 0.456531 |
| MA0063.1 | 0 |
| MA0066.1 | 0.941452 |
| MA0067.1 | 1.65513 |
| MA0068.1 | 1.04561 |
| MA0069.1 | 1.31207 |
| MA0070.1 | 1.30033 |
| MA0071.1 | 0.897953 |
| MA0072.1 | 1.29561 |
| MA0073.1 | 8.86238 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 0.734647 |
| MA0077.1 | 1.28751 |
| MA0078.1 | 1.04495 |
| MA0081.1 | 0.714712 |
| MA0083.1 | 1.33535 |
| MA0084.1 | 1.84562 |
| MA0087.1 | 1.29304 |
| MA0088.1 | 0.715722 |
| MA0089.1 | 0 |
| MA0090.1 | 0.751469 |
| MA0091.1 | 0.829044 |
| MA0092.1 | 0.785956 |
| MA0093.1 | 0.642957 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.956299 |
| MA0101.1 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.846801 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| MA0108.2 | 1.15387 |
| MA0109.1 | 0 |
| MA0111.1 | 0.767139 |
| MA0113.1 | 1.00436 |
| MA0114.1 | 0.549955 |
| MA0115.1 | 1.57693 |
| MA0116.1 | 0.560723 |
| MA0117.1 | 1.36676 |
| MA0119.1 | 0.695578 |
| MA0122.1 | 1.39371 |
| MA0124.1 | 1.53432 |
| MA0125.1 | 1.44766 |
| MA0130.1 | 0 |
| MA0131.1 | 1.06461 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.35921 |
| MA0136.1 | 0.948776 |
| MA0139.1 | 0.440097 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 1.31729 |
| MA0145.1 | 2.11725 |
| MA0146.1 | 2.3244 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 0.449458 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 5.50873 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.731309 |
| MA0065.2 | 1.39232 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.312019 |
| MA0155.1 | 0.711948 |
| MA0156.1 | 0.669101 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 0.565904 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 2.76014 |
| MA0163.1 | 0.776149 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 8.812 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 0.575594 |
| MA0442.1 | 0 |
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 |
|---|---|---|---|---|
| CCNT2#905 | 3 | 6.33620157696263 | 0.00393075003576489 | 0.0189881407486239 |
| E2F6#1876 | 3 | 5.01715573169739 | 0.0079176980688633 | 0.0321882626942006 |
| EGR1#1958 | 3 | 4.98817909481014 | 0.00805648813738344 | 0.0320403474574536 |
| HMGN3#9324 | 3 | 8.17854772335059 | 0.00182776694216421 | 0.0108633138898639 |
| NFKB1#4790 | 3 | 5.48806342419384 | 0.00604938181565543 | 0.0269420634305005 |
| NR3C1#2908 | 2 | 9.98201555411536 | 0.0127847436554717 | 0.0460390953256262 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0276463520597988 |
| TAF7#6879 | 3 | 11.4330694049239 | 0.000669018198194583 | 0.0054243918640823 |
| YY1#7528 | 3 | 4.91117074985386 | 0.00844145534180826 | 0.0329059851613583 |
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.
