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Difference between revisions of "Coexpression cluster:C885"

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|tf_chipseq_enrich=E2F1#1869;6:3.27159280991955:0.00338995924180989:0.0173008186696336!EP300#2033;6:4.51596115081547:0.000579924810993498:0.00486597311282638!FOXA1#3169;6:7.38761316625697:3.56196695095157e-05:0.000689926310071275!FOXA2#3170;6:16.4203091684435:3.37701953018255e-07:1.67789030786268e-05!GATA3#2625;6:18.1576775714707:1.86572751230391e-07:1.01804971607894e-05!HEY1#23462;7:3.14230858908222:0.00125876346284377:0.00845699564464074!HNF4A#3172;5:12.8512724238632:1.64120812799935e-05:0.000378965588503481!MYC#4609;7:4.06177478902954:0.000235555679657337:0.00256743890917686!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728442666109421!RXRA#6256;6:13.3830780927555:1.12450168564813e-06:4.62551522439564e-05!SIN3A#25942;6:3.60592315121009:0.00200305799133432:0.0116466637098856!ZBTB7A#51341;6:4.90127287191726:0.000366991098105653:0.00365622276972778
 
|tf_chipseq_enrich=E2F1#1869;6:3.27159280991955:0.00338995924180989:0.0173008186696336!EP300#2033;6:4.51596115081547:0.000579924810993498:0.00486597311282638!FOXA1#3169;6:7.38761316625697:3.56196695095157e-05:0.000689926310071275!FOXA2#3170;6:16.4203091684435:3.37701953018255e-07:1.67789030786268e-05!GATA3#2625;6:18.1576775714707:1.86572751230391e-07:1.01804971607894e-05!HEY1#23462;7:3.14230858908222:0.00125876346284377:0.00845699564464074!HNF4A#3172;5:12.8512724238632:1.64120812799935e-05:0.000378965588503481!MYC#4609;7:4.06177478902954:0.000235555679657337:0.00256743890917686!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728442666109421!RXRA#6256;6:13.3830780927555:1.12450168564813e-06:4.62551522439564e-05!SIN3A#25942;6:3.60592315121009:0.00200305799133432:0.0116466637098856!ZBTB7A#51341;6:4.90127287191726:0.000366991098105653:0.00365622276972778
 
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 +
|tfbs_overrepresentation_for_novel_motifs=2.30939,0.479568,0.305225,0.440628,1.35412,0.439064,0.511871,0.492582,0.94513,0.527834,0.410439,0.553754,0.127813,0.500805,0.266007,0.287179,0.728104,0.624077,0.137566,0.216842,0.305279,0.940495,0.431698,0.262652,0.347482,0.575764,1.19851,0.429643,0.270022,0.329945,0.389837,0.764231,1.06082,0.129565,0.23642,0.045176,5.39834,0.440165,0.213144,0.14756,0.235191,0.97787,0.366128,0.264644,1.885,0.333541,0.51292,0.4002,0.0372068,0.270138,0.589559,0.524278,0.0739421,0.839846,0.99088,2.17296,0.273964,0.472204,0.100358,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.114787,0.105027,0.684401,0.750836,0.341765,0.141333,0.699894,0.532172,0.166331,2.1596,0.358653,0.214403,5.96664,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,1.95762,0.82268,0.619373,2.70104,0.613956,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,1.30109,1.52941,0.814459,0.812156,1.07582,1.12352,0.232218,0.0867932,0.388709,0.664981,1.09481,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,1.26529,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.193834,0.0656964,1.87005,0.912334,0.918218,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,1.03307,0.510589,1.98286
 
}}
 
}}

Revision as of 05:32, 26 November 2012


Full id: C885_breast_Intestinal_MCF7_Prostate_small_colon_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr11:72493722..72493753,-p9@STARD10
Hg19::chr14:38060540..38060566,-p@chr14:38060540..38060566
-
Hg19::chr14:38061906..38061927,-p@chr14:38061906..38061927
-
Hg19::chr14:38064495..38064506,-p4@FOXA1
Hg19::chr14:38064536..38064550,-p7@FOXA1
Hg19::chr14:38064554..38064559,-p12@FOXA1
Hg19::chr14:38064572..38064584,-p5@FOXA1
Hg19::chr14:38064590..38064606,-p2@FOXA1
Hg19::chr14:38064797..38064843,+p1@TTC6


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:0042593glucose homeostasis0.0231308033864625
GO:0033500carbohydrate homeostasis0.0231308033864625
GO:0048754branching morphogenesis of a tube0.0231308033864625
GO:0001763morphogenesis of a branching structure0.0231308033864625
GO:0030855epithelial cell differentiation0.0231308033864625
GO:0030324lung development0.0231308033864625
GO:0030323respiratory tube development0.0231308033864625
GO:0002009morphogenesis of an epithelium0.029644417655839
GO:0035239tube morphogenesis0.033114259988823
GO:0042445hormone metabolic process0.033114259988823
GO:0035295tube development0.0400073614017467
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0435551382564899



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
epithelial cell6.34e-19253
endodermal cell5.06e-1058
metabolising cell3.64e-0812
endopolyploid cell3.64e-0812
parenchymal cell3.64e-0812
polyploid cell3.64e-0812
hepatocyte3.64e-0812
epithelial cell of prostate8.09e-073
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract6.49e-34118
digestive system3.14e-31145
digestive tract3.14e-31145
primitive gut3.14e-31145
endoderm-derived structure6.35e-28160
endoderm6.35e-28160
presumptive endoderm6.35e-28160
endo-epithelium1.61e-2182
foregut3.20e-2087
subdivision of trunk4.48e-16112
epithelium of foregut-midgut junction1.80e-1525
anatomical boundary1.80e-1525
hepatobiliary system1.80e-1525
foregut-midgut junction1.80e-1525
septum transversum1.80e-1525
trunk region element1.11e-14101
gut epithelium1.50e-1454
epithelial bud9.15e-1437
sac6.96e-1326
digestive tract diverticulum7.17e-1323
organ system subdivision7.95e-13223
respiratory primordium1.73e-1238
endoderm of foregut1.73e-1238
trunk3.55e-12199
epithelial sac1.23e-1125
hepatic diverticulum1.41e-1122
liver primordium1.41e-1122
respiratory tract1.53e-1054
organism subdivision1.97e-10264
immaterial anatomical entity7.18e-10117
epithelial fold8.58e-1047
thoracic segment of trunk8.94e-1052
respiratory system9.88e-1074
multi-tissue structure2.05e-09342
lung3.77e-0922
respiratory tube3.77e-0922
respiration organ3.77e-0922
pair of lungs3.77e-0922
lung primordium3.77e-0922
lung bud3.77e-0922
gland5.47e-0959
hindgut9.08e-0919
abdomen element1.30e-0854
abdominal segment element1.30e-0854
thoracic cavity element1.49e-0834
thoracic cavity1.49e-0834
thoracic segment organ3.27e-0835
cloaca6.09e-0814
anal region6.09e-0814
embryonic cloaca6.09e-0814
terminal part of digestive tract6.09e-0814
primitive urogenital sinus6.09e-0814
proctodeum6.09e-0814
segment of respiratory tract7.05e-0847
intestine7.53e-0817
liver8.12e-0819
digestive gland8.12e-0819
liver bud8.12e-0819
biliary system2.11e-079
biliary tree2.11e-079
biliary bud2.11e-079
genitourinary system2.59e-0715
gastrointestinal system2.69e-0725
abdominal segment of trunk2.76e-0760
abdomen2.76e-0760
Disease
Ontology termp-valuen
carcinoma6.68e-43106
cell type cancer1.18e-27143
cancer2.82e-15235
disease of cellular proliferation1.24e-14239
disease of anatomical entity8.56e-1339
thoracic cancer4.02e-104
breast cancer4.02e-104
squamous cell carcinoma1.82e-0914
respiratory system cancer8.62e-0916
lung carcinoma1.06e-079
lung cancer1.20e-0715


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
E2F1#186963.271592809919550.003389959241809890.0173008186696336
EP300#203364.515961150815470.0005799248109934980.00486597311282638
FOXA1#316967.387613166256973.56196695095157e-050.000689926310071275
FOXA2#3170616.42030916844353.37701953018255e-071.67789030786268e-05
GATA3#2625618.15767757147071.86572751230391e-071.01804971607894e-05
HEY1#2346273.142308589082220.001258763462843770.00845699564464074
HNF4A#3172512.85127242386321.64120812799935e-050.000378965588503481
MYC#460974.061774789029540.0002355556796573370.00256743890917686
POLR2A#543092.147453176558070.001029412892608020.00728442666109421
RXRA#6256613.38307809275551.12450168564813e-064.62551522439564e-05
SIN3A#2594263.605923151210090.002003057991334320.0116466637098856
ZBTB7A#5134164.901272871917260.0003669910981056530.00365622276972778



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.