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{{Coexpression_clusters
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DNA damage checkpoint!0.0286350242431562!5371$GO:0006977!DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest!0.0286350242431562!5371$GO:0042771!DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis!0.0286350242431562!5371$GO:0031575!G1/S transition checkpoint!0.0286350242431562!5371$GO:0016605!PML body!0.0286350242431562!5371$GO:0030330!DNA damage response, signal transduction by p53 class mediator!0.0286350242431562!5371$GO:0016525!negative regulation of angiogenesis!0.0286350242431562!5371$GO:0008630!DNA damage response, signal transduction resulting in induction of apoptosis!0.0286350242431562!5371$GO:0005626!insoluble fraction!0.0286350242431562!5371$GO:0000077!DNA damage checkpoint!0.0300596940472044!5371$GO:0007093!mitotic cell cycle checkpoint!0.0300596940472044!5371$GO:0031570!DNA integrity checkpoint!0.0300596940472044!5371$GO:0008629!induction of apoptosis by intracellular signals!0.0349571040718196!5371$GO:0045765!regulation of angiogenesis!0.0349571040718196!5371$GO:0042770!DNA damage response, signal transduction!0.0369141724117895!5371$GO:0001666!response to hypoxia!0.0379388436354144!5371$GO:0030308!negative regulation of cell growth!0.0379388436354144!5371$GO:0045792!negative regulation of cell size!0.0379388436354144!5371$GO:0000075!cell cycle checkpoint!0.0379388436354144!5371$GO:0045926!negative regulation of growth!0.0392541470303728!5371$GO:0007088!regulation of mitosis!0.0410548490495792!5371|id=C2138|ontology_enrichment_celltype=CL:0002087!3.52e-18!115;CL:0000738!4.20e-18!136;CL:0000766!3.54e-17!72;CL:0002194!3.51e-16!59;CL:0000576!3.51e-16!59;CL:0000040!3.51e-16!59;CL:0000559!3.51e-16!59;CL:0000473!4.82e-16!48;CL:0000234!4.82e-16!48;CL:0002031!8.84e-16!120;CL:0000860!7.66e-15!42;CL:0002057!7.66e-15!42;CL:0002009!1.24e-14!61;CL:0000839!1.64e-14!66;CL:0002320!2.38e-13!361;CL:0000557!4.44e-13!67;CL:0000037!1.40e-12!168;CL:0000566!1.40e-12!168;CL:0000988!2.42e-12!177;CL:0000134!4.26e-12!354;CL:0002032!5.05e-12!161;CL:0000837!5.05e-12!161;CL:0000048!5.56e-12!427;CL:0000723!1.06e-10!433;CL:0000034!3.99e-10!441;CL:0000219!1.94e-09!386;CL:0000763!1.37e-08!108;CL:0000049!1.37e-08!108|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002193!2.07e-19!108;UBERON:0002405!1.37e-17!93;UBERON:0002390!5.18e-17!98;UBERON:0003061!5.18e-17!98;UBERON:0002371!3.04e-13!76;UBERON:0002384!4.98e-13!371;UBERON:0004765!5.26e-11!90;UBERON:0001474!1.04e-10!82;UBERON:0001434!5.94e-10!100;UBERON:0002204!5.05e-09!167;UBERON:0003081!2.37e-08!203;UBERON:0000926!9.34e-07!315;UBERON:0004120!9.34e-07!315;UBERON:0006603!9.34e-07!315|pathway_enrichment=7.03959989046011e-05;0.0222803336533063;2;139;Ubiquitin mediated proteolysis (KEGG):04120!5.70320151504265e-06;0.00361012655902199;3;511;Signaling in Immune system 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|full_id=C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal
|gostat_on_coexpression_clusters=GO:0031571!G1 DNA damage checkpoint!0.0286350242431562!5371$GO:0006977!DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest!0.0286350242431562!5371$GO:0042771!DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis!0.0286350242431562!5371$GO:0031575!G1/S transition checkpoint!0.0286350242431562!5371$GO:0016605!PML body!0.0286350242431562!5371$GO:0030330!DNA damage response, signal transduction by p53 class mediator!0.0286350242431562!5371$GO:0016525!negative regulation of angiogenesis!0.0286350242431562!5371$GO:0008630!DNA damage response, signal transduction resulting in induction of apoptosis!0.0286350242431562!5371$GO:0005626!insoluble fraction!0.0286350242431562!5371$GO:0000077!DNA damage checkpoint!0.0300596940472044!5371$GO:0007093!mitotic cell cycle checkpoint!0.0300596940472044!5371$GO:0031570!DNA integrity checkpoint!0.0300596940472044!5371$GO:0008629!induction of apoptosis by intracellular signals!0.0349571040718196!5371$GO:0045765!regulation of angiogenesis!0.0349571040718196!5371$GO:0042770!DNA damage response, signal transduction!0.0369141724117895!5371$GO:0001666!response to hypoxia!0.0379388436354144!5371$GO:0030308!negative regulation of cell growth!0.0379388436354144!5371$GO:0045792!negative regulation of cell size!0.0379388436354144!5371$GO:0000075!cell cycle checkpoint!0.0379388436354144!5371$GO:0045926!negative regulation of growth!0.0392541470303728!5371$GO:0007088!regulation of mitosis!0.0410548490495792!5371
|id=C2138
|ontology_enrichment_celltype=CL:0002087!8.30e-18!119;CL:0000738!3.21e-17!140;CL:0002057!1.57e-16!42;CL:0002031!9.71e-16!124;CL:0000766!6.30e-15!76;CL:0002194!1.71e-13!63;CL:0000576!1.71e-13!63;CL:0000040!1.71e-13!63;CL:0000559!1.71e-13!63;CL:0000860!2.61e-13!45;CL:0002320!8.48e-13!365;CL:0000839!1.93e-12!70;CL:0002009!3.55e-12!65;CL:0000048!3.85e-12!430;CL:0000037!5.54e-12!172;CL:0000566!5.54e-12!172;CL:0000134!1.11e-11!358;CL:0000988!1.33e-11!182;CL:0002032!2.33e-11!165;CL:0000837!2.33e-11!165;CL:0000557!3.36e-11!71;CL:0000723!5.68e-11!436;CL:0000034!1.70e-10!444;CL:0000219!4.04e-09!390;CL:0000763!5.84e-07!112;CL:0000049!5.84e-07!112
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!3.44e-17!112;UBERON:0002405!4.15e-17!115;UBERON:0002390!8.28e-15!102;UBERON:0003061!8.28e-15!102;UBERON:0002384!1.38e-12!375;UBERON:0002371!2.14e-11!80;UBERON:0001474!4.47e-09!86;UBERON:0003081!3.21e-08!216;UBERON:0002204!3.43e-08!167;UBERON:0004765!4.33e-08!101;UBERON:0001434!4.33e-08!101
|pathway_enrichment=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
}}

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.valueFDRnGenesnPathwayName
7.03959989046011e-050.02228033365330632139Ubiquitin mediated proteolysis (KEGG):04120
5.70320151504265e-060.003610126559021993511Signaling 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 IDGO nameFDR corrected p-value
GO:0031571G1 DNA damage checkpoint0.0286350242431562
GO:0006977DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest0.0286350242431562
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.0286350242431562
GO:0031575G1/S transition checkpoint0.0286350242431562
GO:0016605PML body0.0286350242431562
GO:0030330DNA damage response, signal transduction by p53 class mediator0.0286350242431562
GO:0016525negative regulation of angiogenesis0.0286350242431562
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0286350242431562
GO:0005626insoluble fraction0.0286350242431562
GO:0000077DNA damage checkpoint0.0300596940472044
GO:0007093mitotic cell cycle checkpoint0.0300596940472044
GO:0031570DNA integrity checkpoint0.0300596940472044
GO:0008629induction of apoptosis by intracellular signals0.0349571040718196
GO:0045765regulation of angiogenesis0.0349571040718196
GO:0042770DNA damage response, signal transduction0.0369141724117895
GO:0001666response to hypoxia0.0379388436354144
GO:0030308negative regulation of cell growth0.0379388436354144
GO:0045792negative regulation of cell size0.0379388436354144
GO:0000075cell cycle checkpoint0.0379388436354144
GO:0045926negative regulation of growth0.0392541470303728
GO:0007088regulation of mitosis0.0410548490495792



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>

Cell Type
Ontology termp-valuen
nongranular leukocyte3.52e-18115
leukocyte4.20e-18136
myeloid leukocyte3.54e-1772
monopoietic cell3.51e-1659
monocyte3.51e-1659
monoblast3.51e-1659
promonocyte3.51e-1659
defensive cell4.82e-1648
phagocyte4.82e-1648
hematopoietic lineage restricted progenitor cell8.84e-16120
classical monocyte7.66e-1542
CD14-positive, CD16-negative classical monocyte7.66e-1542
macrophage dendritic cell progenitor1.24e-1461
myeloid lineage restricted progenitor cell1.64e-1466
connective tissue cell2.38e-13361
granulocyte monocyte progenitor cell4.44e-1367
hematopoietic stem cell1.40e-12168
angioblastic mesenchymal cell1.40e-12168
hematopoietic cell2.42e-12177
mesenchymal cell4.26e-12354
hematopoietic oligopotent progenitor cell5.05e-12161
hematopoietic multipotent progenitor cell5.05e-12161
multi fate stem cell5.56e-12427
somatic stem cell1.06e-10433
stem cell3.99e-10441
motile cell1.94e-09386
myeloid cell1.37e-08108
common myeloid progenitor1.37e-08108
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.07e-19108
immune system1.37e-1793
hematopoietic system5.18e-1798
blood island5.18e-1798
bone marrow3.04e-1376
connective tissue4.98e-13371
skeletal element5.26e-1190
bone element1.04e-1082
skeletal system5.94e-10100
musculoskeletal system5.05e-09167
lateral plate mesoderm2.37e-08203
mesoderm9.34e-07315
mesoderm-derived structure9.34e-07315
presumptive mesoderm9.34e-07315


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.13.18613
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.52211
MA0138.20.928035
MA0002.21.75253
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.12.64806
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
EGR1#195844.988179094810140.001615011500076050.0101266922464243
IRF1#365935.727872815172930.008097114790333330.0319839096667028
IRF4#3662210.95725634337210.01174530180688030.0428111393365014
MXI1#460137.471178721569470.003741314738550960.0186199270898034
RAD21#588537.766275421592250.0033411193858720.0172615962177139
SIN3A#2594245.408884726815140.001168172384885160.0079428877412123
SPI1#668836.153242631392040.006580387113059030.0280888155352423
STAT1#6772315.52994062289940.000434088655175550.00404783795159636
STAT2#6773348.94782838983051.42094046481278e-050.000340136606015544
STAT3#677437.889598747865680.003190760481680130.016738991056168
USF1#739134.771124457905970.01370465887188020.0482715884091698
ZBTB7A#5134135.513931980906920.009038352821081090.0342236433282897
ZNF143#7702310.12565741417090.001534861610688180.0097600713442927
ZNF263#1012748.221841637010680.0002187871180958320.00248125831543171



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.

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