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{{Coexpression_clusters
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|full_id=C4849_CD14_Mesothelial_Mast_acute_lymphoma_rhabdomyosarcoma_H9
|id=C4849
|ontology_enrichment_celltype=CL:0000037!3.61e-55!172;CL:0000566!3.61e-55!172;CL:0002032!5.29e-52!165;CL:0000837!5.29e-52!165;CL:0000988!8.63e-51!182;CL:0000738!7.37e-40!140;CL:0002087!1.66e-34!119;CL:0002031!2.77e-34!124;CL:0000763!1.52e-32!112;CL:0000049!1.52e-32!112;CL:0000766!3.16e-21!76;CL:0000860!1.53e-19!45;CL:0002057!2.40e-19!42;CL:0000557!4.73e-18!71;CL:0000839!2.62e-17!70;CL:0000542!6.82e-17!53;CL:0000051!6.82e-17!53;CL:0000838!7.51e-17!52;CL:0002194!5.03e-16!63;CL:0000576!5.03e-16!63;CL:0000040!5.03e-16!63;CL:0000559!5.03e-16!63;CL:0002009!7.93e-16!65;CL:0000063!4.16e-09!578;CL:0000084!1.98e-08!25;CL:0000827!1.98e-08!25;CL:0000945!2.53e-08!24;CL:0000826!2.53e-08!24;CL:0000134!5.63e-07!358
|ontology_enrichment_disease=DOID:2531!3.36e-18!51;DOID:0060083!3.36e-18!51;DOID:1240!9.81e-16!39;DOID:8692!1.22e-13!31;DOID:162!3.58e-13!235;DOID:14566!7.37e-13!239;DOID:0050686!4.49e-11!137;DOID:305!1.40e-07!106
|ontology_enrichment_uberon=UBERON:0002390!1.15e-21!102;UBERON:0003061!1.15e-21!102;UBERON:0002193!1.90e-16!112;UBERON:0002371!1.99e-15!80;UBERON:0001474!6.04e-15!86;UBERON:0004765!7.48e-12!101;UBERON:0001434!7.48e-12!101;UBERON:0002405!3.11e-08!115
}}

Latest revision as of 14:20, 17 September 2013


Full id: C4849_CD14_Mesothelial_Mast_acute_lymphoma_rhabdomyosarcoma_H9



Phase1 CAGE Peaks

Hg19::chrX:131157290..131157309,+p2@MST4
Hg19::chrX:131157322..131157339,+p1@MST4
Hg19::chrX:131157354..131157369,+p3@MST4


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
hematopoietic stem cell1.66e-53168
angioblastic mesenchymal cell1.66e-53168
hematopoietic oligopotent progenitor cell2.32e-50161
hematopoietic multipotent progenitor cell2.32e-50161
hematopoietic cell9.80e-50177
leukocyte4.69e-39136
nongranular leukocyte1.51e-33115
hematopoietic lineage restricted progenitor cell2.62e-33120
myeloid cell2.17e-31108
common myeloid progenitor2.17e-31108
myeloid leukocyte6.41e-2172
classical monocyte2.44e-1842
CD14-positive, CD16-negative classical monocyte2.44e-1842
granulocyte monocyte progenitor cell1.82e-1767
myeloid lineage restricted progenitor cell9.47e-1766
lymphocyte1.28e-1653
common lymphoid progenitor1.28e-1653
lymphoid lineage restricted progenitor cell1.37e-1652
defensive cell2.48e-1648
phagocyte2.48e-1648
nucleate cell4.26e-1655
monopoietic cell1.58e-1559
monocyte1.58e-1559
monoblast1.58e-1559
promonocyte1.58e-1559
macrophage dendritic cell progenitor2.89e-1561
lymphocyte of B lineage1.71e-0824
pro-B cell1.71e-0824
T cell5.07e-0825
pro-T cell5.07e-0825
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.78e-2098
blood island2.78e-2098
hemolymphoid system4.08e-15108
bone marrow1.16e-1476
bone element3.41e-1482
skeletal element4.48e-1390
immune system1.66e-1193
skeletal system1.36e-10100
Disease
Ontology termp-valuen
hematologic cancer1.27e-1751
immune system cancer1.27e-1751
leukemia7.78e-1539
cancer2.26e-13235
myeloid leukemia4.91e-1331
disease of cellular proliferation5.48e-13239
organ system cancer4.41e-11137
carcinoma7.31e-08106


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.78116
MA0074.15.05885
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.13.60951
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.13.70241
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.11.29138
MA0259.10.575594
MA0442.10



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#promotersEnrichmentp-valueq-value
BRCA1#672320.18423064322380.0001215704860271640.001645929477598
CCNT2#90536.336201576962630.003930750035764890.0191448772552931
CHD2#1106310.34402283411690.0009033701102746880.00663388208036691
E2F1#186934.907389214879320.008460985347239390.0328313895106942
E2F6#187635.017155731697390.00791769806886330.0324828718471938
EGR1#195834.988179094810140.008056488137383440.032294909210877
ELF1#199734.258097958807540.01295179875054610.0465459863634522
HMGN3#932438.178547723350590.001827766942164210.0109367567132284
MYC#460935.22228187160940.007020843755740150.0296526165078351
TAL1#6886329.86861667744023.75103522793067e-050.000723728742231389



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.

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