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Coexpression cluster:C515: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:24, 17 September 2013


Full id: C515_Small_Urothelial_Sebocyte_Prostate_Bronchial_Mallassezderived_Esophageal



Phase1 CAGE Peaks

Hg19::chr12:47661665..47661671,+p@chr12:47661665..47661671
+
Hg19::chr21:45020673..45020684,-p@chr21:45020673..45020684
-
Hg19::chr21:45020688..45020711,-p@chr21:45020688..45020711
-
Hg19::chr21:45020721..45020728,-p@chr21:45020721..45020728
-
Hg19::chr4:188228506..188228525,+p@chr4:188228506..188228525
+
Hg19::chr5:146263947..146263959,-p@chr5:146263947..146263959
-
Hg19::chr5:149979871..149979915,+p@chr5:149979871..149979915
+
Hg19::chr5:61213098..61213119,-p@chr5:61213098..61213119
-
Hg19::chr5:61213127..61213133,-p@chr5:61213127..61213133
-
Hg19::chr5:61213156..61213165,-p@chr5:61213156..61213165
-
Hg19::chr5:61213166..61213177,-p@chr5:61213166..61213177
-
Hg19::chr5:61213179..61213189,-p@chr5:61213179..61213189
-
Hg19::chr6:12314459..12314482,-p3@EDN1
Hg19::chr7:150813498..150813509,+p30@AGAP3
Hg19::chr8:123132065..123132067,+p@chr8:123132065..123132067
+
Hg19::chr8:143814087..143814102,-p@chr8:143814087..143814102
-
Hg19::chr9:113802868..113802878,-p@chr9:113802868..113802878
-
Hg19::chrX:102977640..102977644,-p@chrX:102977640..102977644
-


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:0031705bombesin receptor binding0.000917422190823815
GO:0031583G-protein signaling, phospholipase D activating pathway0.000917422190823815
GO:0043179rhythmic excitation0.000917422190823815
GO:0031708endothelin B receptor binding0.000917422190823815
GO:0031707endothelin A receptor binding0.000917422190823815
GO:0060024rhythmic synaptic transmission0.000917422190823815
GO:0030815negative regulation of cAMP metabolic process0.00137613328623572
GO:0030818negative regulation of cAMP biosynthetic process0.00137613328623572
GO:0030809negative regulation of nucleotide biosynthetic process0.00137613328623572
GO:0030803negative regulation of cyclic nucleotide biosynthetic process0.00137613328623572
GO:0042474middle ear morphogenesis0.00137613328623572
GO:0030800negative regulation of cyclic nucleotide metabolic process0.00137613328623572
GO:0030147natriuresis0.00157272375569797
GO:0030817regulation of cAMP biosynthetic process0.00157272375569797
GO:0003091renal water homeostasis0.00157272375569797
GO:0030146diuresis0.00157272375569797
GO:0030802regulation of cyclic nucleotide biosynthetic process0.00157272375569797
GO:0030808regulation of nucleotide biosynthetic process0.00157272375569797
GO:0051482elevation of cytosolic calcium ion concentration during G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.00157272375569797
GO:0045980negative regulation of nucleotide metabolic process0.00157272375569797
GO:0030814regulation of cAMP metabolic process0.00157272375569797
GO:0030799regulation of cyclic nucleotide metabolic process0.00167529269628697
GO:0030104water homeostasis0.00167529269628697
GO:0018987osmoregulation0.00183484438164763
GO:0003014renal system process0.00183484438164763
GO:0019229regulation of vasoconstriction0.00183484438164763
GO:0051899membrane depolarization0.00183484438164763
GO:0006140regulation of nucleotide metabolic process0.00196590469462246
GO:0001569patterning of blood vessels0.00201832881981239
GO:0046888negative regulation of hormone secretion0.00201832881981239
GO:0009405pathogenesis0.0023083526091696
GO:0014032neural crest cell development0.00233525648573335
GO:0014033neural crest cell differentiation0.00233525648573335
GO:0042310vasoconstriction0.00251635800911675
GO:0050804regulation of synaptic transmission0.00251635800911675
GO:0051048negative regulation of secretion0.00259936287400081
GO:0051969regulation of transmission of nerve impulse0.00260741043707821
GO:0007589fluid secretion0.00260741043707821
GO:0046883regulation of hormone secretion0.00261465324384787
GO:0006171cAMP biosynthetic process0.00261465324384787
GO:0046058cAMP metabolic process0.00295365193143277
GO:0048762mesenchymal cell differentiation0.00307229756927045
GO:0014031mesenchymal cell development0.00307229756927045
GO:0031644regulation of neurological process0.00312757565053574
GO:0009880embryonic pattern specification0.00314544751139594
GO:0048754branching morphogenesis of a tube0.00314544751139594
GO:0009953dorsal/ventral pattern formation0.00314544751139594
GO:0007585respiratory gaseous exchange0.00314544751139594
GO:0015758glucose transport0.00314544751139594
GO:0042471ear morphogenesis0.00314544751139594
GO:0042391regulation of membrane potential0.00314544751139594
GO:0001763morphogenesis of a branching structure0.00314544751139594
GO:0008645hexose transport0.00314544751139594
GO:0044403symbiosis, encompassing mutualism through parasitism0.00314544751139594
GO:0044419interspecies interaction between organisms0.00314544751139594
GO:0015749monosaccharide transport0.00314544751139594
GO:0006885regulation of pH0.00318683497865115
GO:0046879hormone secretion0.00322679529186308
GO:0051216cartilage development0.00335869819013465
GO:0007205protein kinase C activation0.0034862043251305
GO:0009190cyclic nucleotide biosynthetic process0.00355677526288618
GO:0007588excretion0.00355677526288618
GO:0035150regulation of tube size0.00355677526288618
GO:0050880regulation of blood vessel size0.00355677526288618
GO:0043583ear development0.00355677526288618
GO:0003018vascular process in circulatory system0.00358628674594764
GO:0001666response to hypoxia0.00394354613369043
GO:0009187cyclic nucleotide metabolic process0.00398879213401659
GO:0001701in utero embryonic development0.00398879213401659
GO:0009890negative regulation of biosynthetic process0.00401044557702982
GO:0008217regulation of blood pressure0.00426407497143464
GO:0051046regulation of secretion0.00451065910488376
GO:0051480cytosolic calcium ion homeostasis0.00506996473876319
GO:0003001generation of a signal involved in cell-cell signaling0.00506996473876319
GO:0007204elevation of cytosolic calcium ion concentration0.00506996473876319
GO:0032147activation of protein kinase activity0.00506996473876319
GO:0035239tube morphogenesis0.00600494524902861
GO:0007423sensory organ development0.00605498645943718
GO:0003002regionalization0.00605498645943718
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.00605498645943718
GO:0048598embryonic morphogenesis0.00622536486630446
GO:0007507heart development0.00622536486630446
GO:0009792embryonic development ending in birth or egg hatching0.00622536486630446
GO:0043009chordate embryonic development0.00622536486630446
GO:0001664G-protein-coupled receptor binding0.0067349582008713
GO:0008643carbohydrate transport0.00710468812893792
GO:0006874cellular calcium ion homeostasis0.00723629638155414
GO:0055074calcium ion homeostasis0.00723629638155414
GO:0035295tube development0.00723629638155414
GO:0006875cellular metal ion homeostasis0.00739856605503077
GO:0055065metal ion homeostasis0.00739856605503077
GO:0007389pattern specification process0.00739856605503077
GO:0050878regulation of body fluid levels0.00739856605503077
GO:0048015phosphoinositide-mediated signaling0.00747457658629087
GO:0001525angiogenesis0.00747457658629087
GO:0045860positive regulation of protein kinase activity0.00808478305663487
GO:0033674positive regulation of kinase activity0.00817167807084306
GO:0051347positive regulation of transferase activity0.00817339770006672
GO:0048514blood vessel morphogenesis0.00817339770006672
GO:0048646anatomical structure formation0.00842193571176262
GO:0008015blood circulation0.00863456179598885
GO:0003013circulatory system process0.00863456179598885
GO:0001568blood vessel development0.00876449937641393
GO:0001944vasculature development0.00878608175058193
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.00943634253418782
GO:0055066di-, tri-valent inorganic cation homeostasis0.00950310910872217
GO:0030003cellular cation homeostasis0.0102888469998933
GO:0055080cation homeostasis0.010346483596513
GO:0001501skeletal development0.0105545635531474
GO:0005179hormone activity0.0107611143464199
GO:0009889regulation of biosynthetic process0.0107611143464199
GO:0008284positive regulation of cell proliferation0.0111502081653971
GO:0005625soluble fraction0.0111502081653971
GO:0009790embryonic development0.0111502081653971
GO:0045859regulation of protein kinase activity0.0111502081653971
GO:0055082cellular chemical homeostasis0.0111502081653971
GO:0006873cellular ion homeostasis0.0111502081653971
GO:0043549regulation of kinase activity0.0112889578057303
GO:0051338regulation of transferase activity0.0114253755193352
GO:0009165nucleotide biosynthetic process0.0116459544223585
GO:0043085positive regulation of catalytic activity0.0116459544223585
GO:0050801ion homeostasis0.0119936169336967
GO:0019932second-messenger-mediated signaling0.0119936169336967
GO:0051239regulation of multicellular organismal process0.0122964167834611
GO:0007268synaptic transmission0.0127705168962675
GO:0048878chemical homeostasis0.0131934048394663
GO:0009888tissue development0.0132195481039967
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0137183286971624
GO:0019226transmission of nerve impulse0.0140813638591562
GO:0051704multi-organism process0.0141000733635845
GO:0009117nucleotide metabolic process0.0142865745746609
GO:0009887organ morphogenesis0.0150957651399192
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.015189200482662
GO:0019725cellular homeostasis0.0153311441666558
GO:0007243protein kinase cascade0.0153311441666558
GO:0031324negative regulation of cellular metabolic process0.0154207877075238
GO:0046903secretion0.0154287644354604
GO:0009892negative regulation of metabolic process0.0173911337043123
GO:0042127regulation of cell proliferation0.0185728492444476
GO:0042592homeostatic process0.0188726850683756
GO:0005615extracellular space0.0206127198619138
GO:0050790regulation of catalytic activity0.0234524123428905
GO:0007267cell-cell signaling0.0246356728165276
GO:0065009regulation of a molecular function0.0256495954184492
GO:0008283cell proliferation0.0282819116757411
GO:0000267cell fraction0.034007458196839
GO:0044421extracellular region part0.034075681373456
GO:0065008regulation of biological quality0.0352437893978223
GO:0048522positive regulation of cellular process0.0352437893978223
GO:0005102receptor binding0.0380546724753719
GO:0009653anatomical structure morphogenesis0.0381671933957299
GO:0048518positive regulation of biological process0.0384593039469036
GO:0048523negative regulation of cellular process0.040783586482986
GO:0048513organ development0.040783586482986
GO:0048519negative regulation of biological process0.0419765043698226
GO:0006950response to stress0.0431188429687193
GO:0048468cell development0.0435454150701852
GO:0050877neurological system process0.0442104592464084



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
respiratory epithelial cell8.03e-4213
endo-epithelial cell4.19e-3942
endodermal cell3.05e-2758
general ecto-epithelial cell1.05e-2414
transitional epithelial cell2.91e-244
urothelial cell2.91e-244
epithelial cell of tracheobronchial tree5.84e-229
epithelial cell of lower respiratory tract5.84e-229
epithelial cell4.88e-21253
bronchial epithelial cell1.29e-173
epithelial cell of Malassez1.61e-173
gingival epithelial cell1.70e-173
mammary gland epithelial cell4.46e-134
sebum secreting cell1.67e-122
epithelial cell of sweat gland1.67e-122
epithelial cell of skin gland1.67e-122
acinar cell of sebaceous gland1.67e-122
epidermal cell1.83e-109
embryonic cell1.29e-09250
ecto-epithelial cell1.82e-0934
epithelial cell of alimentary canal2.20e-0920
stratified squamous epithelial cell4.77e-096
keratin accumulating cell4.77e-096
stratified epithelial cell4.77e-096
keratinizing barrier epithelial cell4.77e-096
epithelial fate stem cell4.77e-096
stratified epithelial stem cell4.77e-096
surface ectodermal cell4.77e-096
duct epithelial cell1.43e-083
branched duct epithelial cell1.43e-083
tracheal epithelial cell1.43e-083
tracheoblast1.43e-083
epithelial cell of prostate2.91e-083
epithelial cell of esophagus7.15e-071
Uber Anatomy
Ontology termp-valuen
urothelium1.91e-195
lower respiratory tract epithelium1.29e-173
epithelium of bronchus1.29e-173
gingival epithelium1.70e-173
transitional epithelium3.15e-166
jaw skeleton2.82e-134
splanchnocranium2.82e-134
mammary gland4.46e-134
mammary bud4.46e-134
mammary ridge4.46e-134
mammary placode4.46e-134
tracheobronchial tree5.78e-1315
lower respiratory tract5.78e-1315
skin gland1.67e-122
epidermis gland1.67e-122
gland of integumental system1.67e-122
sebaceous gland1.67e-122
skin sebaceous gland1.67e-122
sweat gland1.67e-122
sweat gland placode1.67e-122
sebaceous gland placode1.67e-122
endoderm-derived structure3.06e-12160
endoderm3.06e-12160
presumptive endoderm3.06e-12160
bronchus8.86e-115
primary subdivision of cranial skeletal system1.01e-105
epithelial bud1.27e-1037
respiratory system2.99e-1074
epithelial fold6.06e-1047
endo-epithelium4.78e-0982
protuberance5.18e-096
pharyngeal arch5.18e-096
embryonic head5.18e-096
respiratory system epithelium6.43e-0928
respiratory tract1.06e-0854
surface structure3.57e-0899
thoracic cavity element3.30e-0734
thoracic cavity3.30e-0734
mouth mucosa5.32e-0713
thoracic segment organ5.62e-0735
epithelium of mucosa7.42e-078
gingiva7.42e-078
external ectoderm9.08e-078


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)
MA0003.15.5441e-05
MA0004.10.207008
MA0006.10.334079
MA0007.10.193512
MA0009.10.600198
MA0014.18.02757e-05
MA0017.10.125342
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.111328
MA0029.10.522011
MA0030.12.19952
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.628965
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.0114521
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.0063545
MA0056.10
MA0057.10.0104156
MA0058.10.141262
MA0059.10.140431
MA0060.10.0444001
MA0061.11.32241
MA0063.10
MA0066.11.42268
MA0067.10.900956
MA0068.10.0222576
MA0069.10.586593
MA0070.10.576293
MA0071.10.255111
MA0072.10.572162
MA0073.11.60413e-05
MA0074.10.281628
MA0076.10.151641
MA0077.10.565087
MA0078.10.363755
MA0081.10.434032
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.0658118
MA0089.10
MA0090.10.485893
MA0091.10.601165
MA0092.10.181853
MA0093.10.103729
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.11.69535
MA0103.10.658605
MA0105.10.970472
MA0106.10.854542
MA0107.11.31477
MA0108.21.1451
MA0109.10
MA0111.10.170509
MA0113.10.332535
MA0114.10.228885
MA0115.10.827474
MA0116.10.0681676
MA0117.10.635078
MA0119.10.130226
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.0300305
MA0140.10.253051
MA0141.10.139313
MA0142.10.426146
MA0143.10.332682
MA0144.10.459643
MA0145.10.175315
MA0146.10.00856874
MA0147.10.0698742
MA0148.10.225411
MA0149.10.245595
MA0062.20.0323736
MA0035.20.252505
MA0039.29.54563e-05
MA0138.20.364793
MA0002.20.999186
MA0137.23.85561
MA0104.20.0440964
MA0047.20.309071
MA0112.20.00394022
MA0065.20.0827578
MA0150.10.157331
MA0151.10
MA0152.10.258148
MA0153.11.65387
MA0154.10.117204
MA0155.10.146881
MA0156.10.372479
MA0157.10.402372
MA0158.10
MA0159.10.0701863
MA0160.10.666979
MA0161.10
MA0162.10.0280426
MA0163.10.00430547
MA0164.10.342871
MA0080.21.67871
MA0018.20.320136
MA0099.20.716923
MA0079.26.62378e-11
MA0102.21.11935
MA0258.10.053266
MA0259.10.257452
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
STAT3#677474.090903054448870.0008647076743299110.0064538844278812



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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