Coexpression cluster:C2138: Difference between revisions
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Latest revision as of 11:59, 17 September 2013
Full id: C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal
Phase1 CAGE Peaks
| Hg19::chr11:57335090..57335155,- | p1@UBE2L6 |
| Hg19::chr15:74287118..74287142,+ | p2@PML |
| Hg19::chr17:41158760..41158822,+ | p1@IFI35 |
| Hg19::chr17:41158825..41158847,+ | p2@IFI35 |
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 7.03959989046011e-05 | 0.0222803336533063 | 2 | 139 | Ubiquitin mediated proteolysis (KEGG):04120 |
| 5.70320151504265e-06 | 0.00361012655902199 | 3 | 511 | Signaling in Immune system (Reactome):REACT_6900 |
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:0031571 | G1 DNA damage checkpoint | 0.0286350242431562 |
| GO:0006977 | DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest | 0.0286350242431562 |
| GO:0042771 | DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis | 0.0286350242431562 |
| GO:0031575 | G1/S transition checkpoint | 0.0286350242431562 |
| GO:0016605 | PML body | 0.0286350242431562 |
| GO:0030330 | DNA damage response, signal transduction by p53 class mediator | 0.0286350242431562 |
| GO:0016525 | negative regulation of angiogenesis | 0.0286350242431562 |
| GO:0008630 | DNA damage response, signal transduction resulting in induction of apoptosis | 0.0286350242431562 |
| GO:0005626 | insoluble fraction | 0.0286350242431562 |
| GO:0000077 | DNA damage checkpoint | 0.0300596940472044 |
| GO:0007093 | mitotic cell cycle checkpoint | 0.0300596940472044 |
| GO:0031570 | DNA integrity checkpoint | 0.0300596940472044 |
| GO:0008629 | induction of apoptosis by intracellular signals | 0.0349571040718196 |
| GO:0045765 | regulation of angiogenesis | 0.0349571040718196 |
| GO:0042770 | DNA damage response, signal transduction | 0.0369141724117895 |
| GO:0001666 | response to hypoxia | 0.0379388436354144 |
| GO:0030308 | negative regulation of cell growth | 0.0379388436354144 |
| GO:0045792 | negative regulation of cell size | 0.0379388436354144 |
| GO:0000075 | cell cycle checkpoint | 0.0379388436354144 |
| GO:0045926 | negative regulation of growth | 0.0392541470303728 |
| GO:0007088 | regulation of mitosis | 0.0410548490495792 |
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 |
|---|---|---|
| nongranular leukocyte | 3.52e-18 | 115 |
| leukocyte | 4.20e-18 | 136 |
| myeloid leukocyte | 3.54e-17 | 72 |
| monopoietic cell | 3.51e-16 | 59 |
| monocyte | 3.51e-16 | 59 |
| monoblast | 3.51e-16 | 59 |
| promonocyte | 3.51e-16 | 59 |
| defensive cell | 4.82e-16 | 48 |
| phagocyte | 4.82e-16 | 48 |
| hematopoietic lineage restricted progenitor cell | 8.84e-16 | 120 |
| classical monocyte | 7.66e-15 | 42 |
| CD14-positive, CD16-negative classical monocyte | 7.66e-15 | 42 |
| macrophage dendritic cell progenitor | 1.24e-14 | 61 |
| myeloid lineage restricted progenitor cell | 1.64e-14 | 66 |
| connective tissue cell | 2.38e-13 | 361 |
| granulocyte monocyte progenitor cell | 4.44e-13 | 67 |
| hematopoietic stem cell | 1.40e-12 | 168 |
| angioblastic mesenchymal cell | 1.40e-12 | 168 |
| hematopoietic cell | 2.42e-12 | 177 |
| mesenchymal cell | 4.26e-12 | 354 |
| hematopoietic oligopotent progenitor cell | 5.05e-12 | 161 |
| hematopoietic multipotent progenitor cell | 5.05e-12 | 161 |
| multi fate stem cell | 5.56e-12 | 427 |
| somatic stem cell | 1.06e-10 | 433 |
| stem cell | 3.99e-10 | 441 |
| motile cell | 1.94e-09 | 386 |
| myeloid cell | 1.37e-08 | 108 |
| common myeloid progenitor | 1.37e-08 | 108 |
| Ontology term | p-value | n |
|---|---|---|
| hemolymphoid system | 2.07e-19 | 108 |
| immune system | 1.37e-17 | 93 |
| hematopoietic system | 5.18e-17 | 98 |
| blood island | 5.18e-17 | 98 |
| bone marrow | 3.04e-13 | 76 |
| connective tissue | 4.98e-13 | 371 |
| skeletal element | 5.26e-11 | 90 |
| bone element | 1.04e-10 | 82 |
| skeletal system | 5.94e-10 | 100 |
| musculoskeletal system | 5.05e-09 | 167 |
| lateral plate mesoderm | 2.37e-08 | 203 |
| mesoderm | 9.34e-07 | 315 |
| mesoderm-derived structure | 9.34e-07 | 315 |
| presumptive mesoderm | 9.34e-07 | 315 |
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 | 0.443649 |
| MA0004.1 | 0.71247 |
| MA0006.1 | 0.532262 |
| MA0007.1 | 0.6918 |
| MA0009.1 | 1.20602 |
| MA0014.1 | 0.524262 |
| MA0017.1 | 0.577281 |
| MA0019.1 | 0.873355 |
| MA0024.1 | 1.09684 |
| MA0025.1 | 1.34373 |
| MA0027.1 | 2.83281 |
| MA0028.1 | 0.550763 |
| MA0029.1 | 1.11704 |
| MA0030.1 | 1.10506 |
| MA0031.1 | 1.03735 |
| MA0038.1 | 0.824639 |
| MA0040.1 | 1.12314 |
| MA0041.1 | 0.732902 |
| MA0042.1 | 0.697662 |
| MA0043.1 | 1.20635 |
| MA0046.1 | 1.19471 |
| MA0048.1 | 0.25531 |
| MA0050.1 | 1.66718 |
| MA0051.1 | 3.18613 |
| MA0052.1 | 1.12718 |
| MA0055.1 | 0.125954 |
| MA0056.1 | 0 |
| MA0057.1 | 0.248209 |
| MA0058.1 | 0.605914 |
| MA0059.1 | 0.604454 |
| MA0060.1 | 0.393285 |
| MA0061.1 | 0.946082 |
| MA0063.1 | 0 |
| MA0066.1 | 0.825101 |
| MA0067.1 | 1.53181 |
| MA0068.1 | 0.313194 |
| MA0069.1 | 1.19071 |
| MA0070.1 | 1.17908 |
| MA0071.1 | 0.782546 |
| MA0072.1 | 1.1744 |
| MA0073.1 | 0.599068 |
| MA0074.1 | 0.819248 |
| MA0076.1 | 0.623864 |
| MA0077.1 | 1.16637 |
| MA0078.1 | 0.926725 |
| MA0081.1 | 0.604638 |
| MA0083.1 | 1.21381 |
| MA0084.1 | 1.72172 |
| MA0087.1 | 1.17185 |
| MA0088.1 | 0.536981 |
| MA0089.1 | 0 |
| MA0090.1 | 0.640115 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 0.535768 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.83965 |
| MA0101.1 | 0.539569 |
| MA0103.1 | 0.521546 |
| MA0105.1 | 1.22348 |
| MA0106.1 | 0.869173 |
| MA0107.1 | 0.453492 |
| MA0108.2 | 1.03412 |
| MA0109.1 | 0 |
| MA0111.1 | 0.655276 |
| MA0113.1 | 0.886811 |
| MA0114.1 | 0.447443 |
| MA0115.1 | 1.45393 |
| MA0116.1 | 0.457606 |
| MA0117.1 | 1.24497 |
| MA0119.1 | 0.586221 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 0.94608 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 1.63368 |
| MA0140.1 | 0.779643 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 0.887001 |
| MA0144.1 | 0.430413 |
| MA0145.1 | 0.195821 |
| MA0146.1 | 0.481 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.353589 |
| MA0035.2 | 0.778873 |
| MA0039.2 | 2.52211 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 1.75253 |
| MA0137.2 | 2.35208 |
| MA0104.2 | 0.392359 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 0.187982 |
| MA0065.2 | 0.199162 |
| MA0150.1 | 0.633493 |
| MA0151.1 | 0 |
| MA0152.1 | 0.78681 |
| MA0153.1 | 1.30799 |
| MA0154.1 | 2.64806 |
| MA0155.1 | 1.61785 |
| MA0156.1 | 0.560797 |
| MA0157.1 | 0.97481 |
| MA0158.1 | 0 |
| MA0159.1 | 0.462502 |
| MA0160.1 | 0.756582 |
| MA0161.1 | 0 |
| MA0162.1 | 0.640035 |
| MA0163.1 | 1.37853 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 0.535868 |
| MA0018.2 | 0.870662 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 1.38179 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 0.418966 |
| MA0259.1 | 0.471671 |
| 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 |
|---|---|---|---|---|
| EGR1#1958 | 4 | 4.98817909481014 | 0.00161501150007605 | 0.0101266922464243 |
| IRF1#3659 | 3 | 5.72787281517293 | 0.00809711479033333 | 0.0319839096667028 |
| IRF4#3662 | 2 | 10.9572563433721 | 0.0117453018068803 | 0.0428111393365014 |
| MXI1#4601 | 3 | 7.47117872156947 | 0.00374131473855096 | 0.0186199270898034 |
| RAD21#5885 | 3 | 7.76627542159225 | 0.003341119385872 | 0.0172615962177139 |
| SIN3A#25942 | 4 | 5.40888472681514 | 0.00116817238488516 | 0.0079428877412123 |
| SPI1#6688 | 3 | 6.15324263139204 | 0.00658038711305903 | 0.0280888155352423 |
| STAT1#6772 | 3 | 15.5299406228994 | 0.00043408865517555 | 0.00404783795159636 |
| STAT2#6773 | 3 | 48.9478283898305 | 1.42094046481278e-05 | 0.000340136606015544 |
| STAT3#6774 | 3 | 7.88959874786568 | 0.00319076048168013 | 0.016738991056168 |
| USF1#7391 | 3 | 4.77112445790597 | 0.0137046588718802 | 0.0482715884091698 |
| ZBTB7A#51341 | 3 | 5.51393198090692 | 0.00903835282108109 | 0.0342236433282897 |
| ZNF143#7702 | 3 | 10.1256574141709 | 0.00153486161068818 | 0.0097600713442927 |
| ZNF263#10127 | 4 | 8.22184163701068 | 0.000218787118095832 | 0.00248125831543171 |
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.
