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Coexpression cluster:C672: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002204!2.47e-20!167;UBERON:0003081!7.15e-19!216;UBERON:0000926!1.55e-16!448;UBERON:0004120!1.55e-16!448;UBERON:0006603!1.55e-16!448;UBERON:0002371!4.42e-12!80;UBERON:0004765!2.61e-11!101;UBERON:0001434!2.61e-11!101;UBERON:0001474!5.48e-11!86;UBERON:0002384!1.67e-09!375;UBERON:0000486!5.10e-09!82;UBERON:0000914!2.23e-08!83;UBERON:0002329!2.23e-08!83;UBERON:0003077!2.23e-08!83;UBERON:0003059!2.23e-08!83;UBERON:0007282!2.23e-08!83;UBERON:0009618!2.23e-08!83;UBERON:0007285!2.23e-08!83;UBERON:0001637!3.54e-08!42;UBERON:0003509!3.54e-08!42;UBERON:0004572!3.54e-08!42;UBERON:0000468!4.64e-08!659;UBERON:0000480!4.99e-08!626;UBERON:0000467!5.20e-08!625;UBERON:0004290!7.67e-08!70;UBERON:0001134!7.86e-08!61;UBERON:0002036!7.86e-08!61;UBERON:0003082!7.86e-08!61;UBERON:0002385!8.29e-08!63;UBERON:0001015!8.29e-08!63;UBERON:0000383!8.29e-08!63;UBERON:0000055!1.16e-07!69;UBERON:0004872!1.35e-07!84;UBERON:0002193!1.43e-07!112;UBERON:0002405!1.98e-07!115;UBERON:0002390!2.53e-07!102;UBERON:0003061!2.53e-07!102;UBERON:0002049!3.03e-07!79;UBERON:0007798!3.03e-07!79;UBERON:0005256!6.33e-07!143;UBERON:0001981!6.62e-07!60;UBERON:0007500!6.62e-07!60;UBERON:0004537!6.62e-07!60;UBERON:0006965!6.62e-07!60;UBERON:0004573!7.97e-07!33;UBERON:0004571!7.97e-07!33
|ontology_enrichment_uberon=UBERON:0002204!2.47e-20!167;UBERON:0003081!7.15e-19!216;UBERON:0000926!1.55e-16!448;UBERON:0004120!1.55e-16!448;UBERON:0006603!1.55e-16!448;UBERON:0002371!4.42e-12!80;UBERON:0004765!2.61e-11!101;UBERON:0001434!2.61e-11!101;UBERON:0001474!5.48e-11!86;UBERON:0002384!1.67e-09!375;UBERON:0000486!5.10e-09!82;UBERON:0000914!2.23e-08!83;UBERON:0002329!2.23e-08!83;UBERON:0003077!2.23e-08!83;UBERON:0003059!2.23e-08!83;UBERON:0007282!2.23e-08!83;UBERON:0009618!2.23e-08!83;UBERON:0007285!2.23e-08!83;UBERON:0001637!3.54e-08!42;UBERON:0003509!3.54e-08!42;UBERON:0004572!3.54e-08!42;UBERON:0000468!4.64e-08!659;UBERON:0000480!4.99e-08!626;UBERON:0000467!5.20e-08!625;UBERON:0004290!7.67e-08!70;UBERON:0001134!7.86e-08!61;UBERON:0002036!7.86e-08!61;UBERON:0003082!7.86e-08!61;UBERON:0002385!8.29e-08!63;UBERON:0001015!8.29e-08!63;UBERON:0000383!8.29e-08!63;UBERON:0000055!1.16e-07!69;UBERON:0004872!1.35e-07!84;UBERON:0002193!1.43e-07!112;UBERON:0002405!1.98e-07!115;UBERON:0002390!2.53e-07!102;UBERON:0003061!2.53e-07!102;UBERON:0002049!3.03e-07!79;UBERON:0007798!3.03e-07!79;UBERON:0005256!6.33e-07!143;UBERON:0001981!6.62e-07!60;UBERON:0007500!6.62e-07!60;UBERON:0004537!6.62e-07!60;UBERON:0006965!6.62e-07!60;UBERON:0004573!7.97e-07!33;UBERON:0004571!7.97e-07!33
|tf_chipseq_enrich=JUNB#3726;3:7.06399215226642:0.007792750127433:0.0320180585608787!POLR2A#5430;13:2.14745317655807:4.83928878402115e-05:0.000841089168437984!POU2F2#5452;5:3.50235540682405:0.00961613860265682:0.0361909873701937!ZBTB33#10009;3:7.30724423768796:0.00709817327748382:0.0295974016419984
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}}
}}

Revision as of 12:48, 5 September 2012


Full id: C672_CD14_Smooth_Mesenchymal_Placental_Fibroblast_mesenchymal_Alveolar



Phase1 CAGE Peaks

Hg19::chr6:36646476..36646498,+p1@CDKN1A
Hg19::chr6:36646510..36646519,+p2@CDKN1A
Hg19::chr6:36652080..36652094,+p1@BC037414
Hg19::chr6:36652270..36652284,+p4@BC037414
Hg19::chr6:36652291..36652299,+p5@BC037414
Hg19::chr6:36653519..36653558,+p@chr6:36653519..36653558
+
Hg19::chr6:36653561..36653579,+p@chr6:36653561..36653579
+
Hg19::chr6:36653603..36653637,+p@chr6:36653603..36653637
+
Hg19::chr6:36653937..36653958,+p@chr6:36653937..36653958
+
Hg19::chr6:36653968..36653983,+p@chr6:36653968..36653983
+
Hg19::chr6:36654158..36654169,+p@chr6:36654158..36654169
+
Hg19::chr6:36654222..36654237,+p@chr6:36654222..36654237
+
Hg19::chr6:36654635..36654646,+p@chr6:36654635..36654646
+


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 IDGO nameFDR corrected p-value
GO:0043071positive regulation of non-apoptotic programmed cell death0.00326739667961851
GO:0016244non-apoptotic programmed cell death0.00326739667961851
GO:0030332cyclin binding0.00326739667961851
GO:0043070regulation of non-apoptotic programmed cell death0.00326739667961851
GO:0000307cyclin-dependent protein kinase holoenzyme complex0.00435652890615801
GO:0045736negative regulation of cyclin-dependent protein kinase activity0.00435652890615801
GO:0030890positive regulation of B cell proliferation0.00435652890615801
GO:0030888regulation of B cell proliferation0.00435652890615801
GO:0048146positive regulation of fibroblast proliferation0.00435652890615801
GO:0048145regulation of fibroblast proliferation0.00435652890615801
GO:0048144fibroblast proliferation0.00435652890615801
GO:0042326negative regulation of phosphorylation0.00435652890615801
GO:0045936negative regulation of phosphate metabolic process0.00435652890615801
GO:0031668cellular response to extracellular stimulus0.00435652890615801
GO:0004861cyclin-dependent protein kinase inhibitor activity0.00435652890615801
GO:0000086G2/M transition of mitotic cell cycle0.00435652890615801
GO:0050871positive regulation of B cell activation0.00435652890615801
GO:0042100B cell proliferation0.00435652890615801
GO:0051716cellular response to stimulus0.00544566113269752
GO:0050864regulation of B cell activation0.00544566113269752
GO:0032946positive regulation of mononuclear cell proliferation0.00594072123567002
GO:0050671positive regulation of lymphocyte proliferation0.00594072123567002
GO:0009411response to UV0.00617174928372385
GO:0000082G1/S transition of mitotic cell cycle0.00617174928372385
GO:0008629induction of apoptosis by intracellular signals0.00627340162486754
GO:0004860protein kinase inhibitor activity0.00630945565719436
GO:0019210kinase inhibitor activity0.00630945565719436
GO:0050670regulation of lymphocyte proliferation0.00630945565719436
GO:0032944regulation of mononuclear cell proliferation0.00630945565719436
GO:0000079regulation of cyclin-dependent protein kinase activity0.00664370658189097
GO:0051251positive regulation of lymphocyte activation0.00664370658189097
GO:0032943mononuclear cell proliferation0.00664370658189097
GO:0030308negative regulation of cell growth0.00664370658189097
GO:0046651lymphocyte proliferation0.00664370658189097
GO:0045792negative regulation of cell size0.00664370658189097
GO:0006469negative regulation of protein kinase activity0.00664370658189097
GO:0033673negative regulation of kinase activity0.00664370658189097
GO:0051348negative regulation of transferase activity0.00664370658189097
GO:0042113B cell activation0.00664370658189097
GO:0045926negative regulation of growth0.00664370658189097
GO:0042325regulation of phosphorylation0.00680043536571006
GO:0009991response to extracellular stimulus0.00683182942102052
GO:0051174regulation of phosphorus metabolic process0.00683182942102052
GO:0019220regulation of phosphate metabolic process0.00683182942102052
GO:0051249regulation of lymphocyte activation0.00735769326373353
GO:0050865regulation of cell activation0.0075080604552936
GO:0009416response to light stimulus0.0075080604552936
GO:0051329interphase of mitotic cell cycle0.00771468660465481
GO:0043086negative regulation of catalytic activity0.00773506152726014
GO:0051325interphase0.00784175203108442
GO:0009314response to radiation0.00846171960619152
GO:0007050cell cycle arrest0.00846171960619152
GO:0019887protein kinase regulator activity0.00863085915370927
GO:0019207kinase regulator activity0.0098425282694681
GO:0046649lymphocyte activation0.012277490553718
GO:0001558regulation of cell growth0.0126028157642428
GO:0009628response to abiotic stimulus0.0126110047283521
GO:0045321leukocyte activation0.0135202621225593
GO:0016049cell growth0.0144990727658071
GO:0040008regulation of growth0.0144990727658071
GO:0008361regulation of cell size0.0144990727658071
GO:0001775cell activation0.0144990727658071
GO:0006917induction of apoptosis0.0144990727658071
GO:0012502induction of programmed cell death0.0144990727658071
GO:0045786negative regulation of progression through cell cycle0.0147111773207944
GO:0008285negative regulation of cell proliferation0.0147111773207944
GO:0043066negative regulation of apoptosis0.0147111773207944
GO:0043069negative regulation of programmed cell death0.0147111773207944
GO:0008284positive regulation of cell proliferation0.0147111773207944
GO:0045859regulation of protein kinase activity0.0147499621537064
GO:0043549regulation of kinase activity0.0148490140181724
GO:0051338regulation of transferase activity0.0149453144419587
GO:0043065positive regulation of apoptosis0.0151889791593077
GO:0043068positive regulation of programmed cell death0.0151889791593077
GO:0051239regulation of multicellular organismal process0.0160901134267436
GO:0000278mitotic cell cycle0.0186872160974673
GO:0000074regulation of progression through cell cycle0.0199721390113478
GO:0051726regulation of cell cycle0.0200512035552657
GO:0022403cell cycle phase0.0203488502072444
GO:0031324negative regulation of cellular metabolic process0.0207479689155775
GO:0004857enzyme inhibitor activity0.0215675073008563
GO:0009892negative regulation of metabolic process0.0231639829644499
GO:0006974response to DNA damage stimulus0.0235147584332384
GO:0042127regulation of cell proliferation0.0242141955481806
GO:0000902cell morphogenesis0.0242141955481806
GO:0032989cellular structure morphogenesis0.0242141955481806
GO:0009719response to endogenous stimulus0.0264896987512366
GO:0005829cytosol0.0278817849994113
GO:0042981regulation of apoptosis0.0278817849994113
GO:0043067regulation of programmed cell death0.0278817849994113
GO:0050790regulation of catalytic activity0.0289637361343472
GO:0022402cell cycle process0.0295959844168343
GO:0009605response to external stimulus0.0296525031999787
GO:0065009regulation of a molecular function0.0310982010216173
GO:0008283cell proliferation0.0341643582640812
GO:0007049cell cycle0.0380742474194434
GO:0006915apoptosis0.0383196726235531
GO:0012501programmed cell death0.0383196726235531
GO:0008219cell death0.0395572824679148
GO:0016265death0.0395572824679148
GO:0065008regulation of biological quality0.0407463585928896
GO:0048522positive regulation of cellular process0.0407463585928896
GO:0009653anatomical structure morphogenesis0.0442843278130819
GO:0048518positive regulation of biological process0.0444868624840366
GO:0048523negative regulation of cellular process0.0471749844409682
GO:0004672protein kinase activity0.0475930233333111
GO:0048519negative regulation of biological process0.0481253940848483
GO:0006950response to stress0.0492933178085657
GO:0048468cell development0.0496404486371399



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
somatic cell6.08e-36591
animal cell3.98e-28679
eukaryotic cell3.98e-28679
CD14-positive, CD16-negative classical monocyte2.76e-1842
somatic stem cell2.21e-17436
multi fate stem cell3.50e-17430
native cell1.93e-16722
classical monocyte6.63e-1645
stem cell8.68e-16444
macrophage dendritic cell progenitor9.31e-1365
monopoietic cell4.35e-1263
monocyte4.35e-1263
monoblast4.35e-1263
promonocyte4.35e-1263
granulocyte monocyte progenitor cell4.51e-1271
myeloid leukocyte4.70e-1176
myeloid lineage restricted progenitor cell1.13e-1070
connective tissue cell3.23e-10365
non-terminally differentiated cell6.40e-10180
smooth muscle cell1.07e-0942
smooth muscle myoblast1.07e-0942
mesenchymal cell1.53e-09358
contractile cell6.82e-0959
muscle precursor cell3.21e-0857
myoblast3.21e-0857
multi-potent skeletal muscle stem cell3.21e-0857
muscle cell3.62e-0854
mesodermal cell5.84e-08119
vascular associated smooth muscle cell1.20e-0732
fibroblast4.24e-0775
motile cell4.35e-07390
embryonic cell5.10e-07248
Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.47e-20167
lateral plate mesoderm7.15e-19216
mesoderm1.55e-16448
mesoderm-derived structure1.55e-16448
presumptive mesoderm1.55e-16448
bone marrow4.42e-1280
skeletal element2.61e-11101
skeletal system2.61e-11101
bone element5.48e-1186
connective tissue1.67e-09375
multilaminar epithelium5.10e-0982
somite2.23e-0883
paraxial mesoderm2.23e-0883
presomitic mesoderm2.23e-0883
presumptive segmental plate2.23e-0883
trunk paraxial mesoderm2.23e-0883
presumptive paraxial mesoderm2.23e-0883
artery3.54e-0842
arterial blood vessel3.54e-0842
arterial system3.54e-0842
multi-cellular organism4.64e-08659
anatomical group4.99e-08626
anatomical system5.20e-08625
dermomyotome7.67e-0870
skeletal muscle tissue7.86e-0861
striated muscle tissue7.86e-0861
myotome7.86e-0861
muscle tissue8.29e-0863
musculature8.29e-0863
musculature of body8.29e-0863
vessel1.16e-0769
splanchnic layer of lateral plate mesoderm1.35e-0784
hemolymphoid system1.43e-07112
immune system1.98e-07115
hematopoietic system2.53e-07102
blood island2.53e-07102
vasculature3.03e-0779
vascular system3.03e-0779
trunk mesenchyme6.33e-07143
blood vessel6.62e-0760
epithelial tube open at both ends6.62e-0760
blood vasculature6.62e-0760
vascular cord6.62e-0760
systemic artery7.97e-0733
systemic arterial system7.97e-0733


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)

{{{tfbs_overrepresentation_jaspar}}}



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
JUNB#372637.063992152266420.0077927501274330.0320180585608787
POLR2A#5430132.147453176558074.83928878402115e-050.000841089168437984
POU2F2#545253.502355406824050.009616138602656820.0361909873701937
ZBTB33#1000937.307244237687960.007098173277483820.0295974016419984



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.