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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.25533303526427,0.

Latest revision as of 11:28, 17 September 2013


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 cell1.14e-34588
animal cell1.48e-28679
eukaryotic cell1.48e-28679
stuff accumulating cell6.20e-1987
defensive cell4.44e-1848
phagocyte4.44e-1848
classical monocyte8.64e-1842
CD14-positive, CD16-negative classical monocyte8.64e-1842
native cell6.19e-17722
somatic stem cell1.57e-16433
multi fate stem cell4.88e-16427
stem cell6.45e-15441
macrophage dendritic cell progenitor1.66e-1361
monopoietic cell7.10e-1359
monocyte7.10e-1359
monoblast7.10e-1359
promonocyte7.10e-1359
granulocyte monocyte progenitor cell1.87e-1267
myeloid lineage restricted progenitor cell2.91e-1166
myeloid leukocyte4.95e-1172
smooth muscle cell1.14e-0943
smooth muscle myoblast1.14e-0943
connective tissue cell1.66e-09361
mesenchymal cell9.97e-09354
embryonic cell4.13e-08250
contractile cell4.34e-0859
fibroblast6.18e-0876
mesodermal cell9.29e-08121
muscle precursor cell1.84e-0758
myoblast1.84e-0758
multi-potent skeletal muscle stem cell1.84e-0758
muscle cell1.86e-0755
vascular associated smooth muscle cell2.29e-0732
motile cell9.81e-07386
Uber Anatomy
Ontology termp-valuen
mesoderm8.95e-21315
mesoderm-derived structure8.95e-21315
presumptive mesoderm8.95e-21315
musculoskeletal system1.39e-19167
lateral plate mesoderm3.15e-15203
bone marrow8.70e-1276
skeletal element1.14e-1190
skeletal system2.97e-11100
bone element1.53e-1082
immune system3.44e-0993
connective tissue5.29e-09371
multilaminar epithelium2.95e-0883
multi-cellular organism3.75e-08656
artery3.87e-0842
arterial blood vessel3.87e-0842
arterial system3.87e-0842
anatomical system4.55e-08624
anatomical group4.88e-08625
vessel2.45e-0768
muscle tissue3.50e-0764
musculature3.50e-0764
musculature of body3.50e-0764
skeletal muscle tissue4.03e-0762
striated muscle tissue4.03e-0762
myotome4.03e-0762
hemolymphoid system4.28e-07108
epithelial vesicle4.49e-0778
splanchnic layer of lateral plate mesoderm6.43e-0783
systemic artery6.43e-0733
systemic arterial system6.43e-0733
somite6.84e-0771
presomitic mesoderm6.84e-0771
presumptive segmental plate6.84e-0771
dermomyotome6.84e-0771
trunk paraxial mesoderm6.84e-0771
dense mesenchyme tissue7.13e-0773
hematopoietic system8.54e-0798
blood island8.54e-0798
vasculature9.88e-0778
vascular system9.88e-0778


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)
MA0003.10.0652591
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.54491
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.11.39986
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.11.73714
MA0050.10.287284
MA0051.10.383704
MA0052.11.57036
MA0055.10.183899
MA0056.10
MA0057.10.123867
MA0058.10.625569
MA0059.10.623149
MA0060.10.622587
MA0061.10.542967
MA0063.10
MA0066.12.67555
MA0067.11.03434
MA0068.10.0529803
MA0069.10.710614
MA0070.10.69985
MA0071.10.930644
MA0072.10.695528
MA0073.10.0028571
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.11.82632
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.12.01936
MA0089.10
MA0090.10.243681
MA0091.10.812021
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.11.82424
MA0101.10.17426
MA0103.10.489275
MA0105.10.10818
MA0106.11.90842
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.11.30787
MA0113.10.439505
MA0114.10.118142
MA0115.10.959312
MA0116.10.391626
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.11.02008
MA0139.13.02309
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.11.17643
MA0145.10.194261
MA0146.11.14469
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.20.224942
MA0138.20.474787
MA0002.20.0821804
MA0137.20.54754
MA0104.20.298328
MA0047.20.413608
MA0112.26.90365
MA0065.20.641236
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.11.54414
MA0155.10.167839
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.795271
MA0160.10.332385
MA0161.10
MA0162.10.350522
MA0163.12.79674
MA0164.10.450848
MA0080.20.985821
MA0018.20.425847
MA0099.20.356906
MA0079.20.022543
MA0102.21.25596
MA0258.12.93741
MA0259.10.132107
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
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.

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