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Coexpression cluster:C221: Difference between revisions

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|tf_chipseq_enrich=JUN#3725;16:3.08008103195971:3.99486758543661e-05:0.000741988219376515!STAT3#6774;19:3.0749205376297:6.20075441492697e-06:0.000183196772373567!TCF7L2#6934;19:3.14820545691707:4.39975432367538e-06:0.000137782891097551
|tf_chipseq_enrich=JUN#3725;16:3.08008103195971:3.99486758543661e-05:0.000741988219376515!STAT3#6774;19:3.0749205376297:6.20075441492697e-06:0.000183196772373567!TCF7L2#6934;19:3.14820545691707:4.39975432367538e-06:0.000137782891097551
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|tfbs_overrepresentation_for_novel_motifs=0.0654535,0.000345545,0.018909,0.953005,0.688262,0.0771058,0.0316276,0.856487,0.132994,0.00512097,0.161767,1.47236,0.000244017,0.0290128,0.928613,1.06961,0.355927,0.180925,1.01417,0.2098,0.641051,0.000351274,0.0726528,0.664228,0.0949159,0.0494286,0.203539,0.015384,0.185775,0.330115,0.137901,0.128219,0.0623141,0.288156,0.0060222,0.091282,0.0216478,0.387193,0.601455,0.02473,0.52602,0.00835189,0.0185915,0.468135,0.00128186,0.00483659,0.0318826,0.302439,0.0130354,0.0942505,0.439607,0.0347229,0.237068,0.169854,0.267067,0.0296663,0.981025,0.244153,0.937707,0.0226911,0.457218,0.131578,0.133951,0.32224,0.146045,0.0829343,0.330565,0.634378,0.123009,1.23715,0.00715504,0.513363,0.00832531,0.733624,0.000208775,0.00301543,0.0636735,0.090229,0.1214,0.350393,0.238876,0.0970929,0.0367823,0.0386557,0.231091,3.45039e-09,0.000100537,0.087042,0.224641,0.723693,0.402373,0.612475,0.424739,3.66397,0.181628,1.28066,0.32414,0.159951,0.0642342,0.00686888,0.282678,0.826616,0.156836,0.360483,0.269465,0.012037,0.104574,0.117558,0.00586497,0.00825041,0.0681044,0.1553,0.24943,0.0138501,0.364896,0.213777,8.87833e-07,0.480317,0.279688,0.521776,0.259994,2.93199,1.29729,0.356681,0.452854,1.05165,0.862275,0.431381,0.289757,0.0381311,2.54275,3.27739,0.811898,0.152397,0.412612,0.0210148,0.467217,0.365228,0.379168,1.15303,0.77165,0.350478,0.547471,0.157978,0.572356,0.0933417,0.0725454,0.999919,0.956405,0.0287518,0.00556934,8.50316e-06,0.614086,0.11813,0.894327,0.520049,0.457488,0.0774772,0.577423,0.00400495,0.349556,1.74109,0.121011,0.0242009,0.0855319,0.954776,0.0548396,0.555503,8.7893e-06
}}
}}

Revision as of 13:50, 26 November 2012


Full id: C221_alveolar_Osteoblast_Myoblast_mesenchymal_liposarcoma_Smooth_hepatocellular



Phase1 CAGE Peaks

Hg19::chr10:101690855..101690861,-p14@DNMBP
Hg19::chr10:101691056..101691064,-p13@DNMBP
Hg19::chr10:101691084..101691100,-p8@DNMBP
Hg19::chr10:101691101..101691115,-p7@DNMBP
Hg19::chr10:101691118..101691135,-p6@DNMBP
Hg19::chr10:101691199..101691208,-p11@DNMBP
Hg19::chr11:104005546..104005596,-p@chr11:104005546..104005596
-
Hg19::chr11:47256459..47256470,+p@chr11:47256459..47256470
+
Hg19::chr12:20910262..20910266,-p@chr12:20910262..20910266
-
Hg19::chr12:92081022..92081033,-p@chr12:92081022..92081033
-
Hg19::chr13:24144882..24144893,+p8@TNFRSF19
Hg19::chr13:24144896..24144956,+p3@TNFRSF19
Hg19::chr13:24144958..24144969,+p10@TNFRSF19
Hg19::chr14:29047309..29047323,+p@chr14:29047309..29047323
+
Hg19::chr15:79290919..79290969,+p@chr15:79290919..79290969
+
Hg19::chr16:11118533..11118538,+p12@CLEC16A
Hg19::chr16:15991751..15991767,-p@chr16:15991751..15991767
-
Hg19::chr17:13574618..13574636,-p@chr17:13574618..13574636
-
Hg19::chr17:40481474..40481498,-p@chr17:40481474..40481498
-
Hg19::chr17:63511856..63511858,-p@chr17:63511856..63511858
-
Hg19::chr18:20715474..20715486,+p4@CABLES1
Hg19::chr18:56199164..56199168,-p@chr18:56199164..56199168
-
Hg19::chr1:114430113..114430124,-p4@BCL2L15
Hg19::chr1:145683530..145683562,+p@chr1:145683530..145683562
+
Hg19::chr1:219980111..219980117,-p@chr1:219980111..219980117
-
Hg19::chr1:246033769..246033788,-p@chr1:246033769..246033788
-
Hg19::chr20:2779140..2779150,-p9@CPXM1
Hg19::chr20:2779199..2779205,-p13@CPXM1
Hg19::chr20:2779236..2779242,-p12@CPXM1
Hg19::chr20:2779313..2779314,-p16@CPXM1
Hg19::chr2:75751179..75751194,+p1@BC018659
Hg19::chr3:165178296..165178305,+p@chr3:165178296..165178305
+
Hg19::chr3:165178316..165178330,+p@chr3:165178316..165178330
+
Hg19::chr3:165178334..165178342,+p@chr3:165178334..165178342
+
Hg19::chr3:55001120..55001131,-p6@LRTM1
Hg19::chr3:55002066..55002104,+p@chr3:55002066..55002104
+
Hg19::chr3:55002159..55002164,+p@chr3:55002159..55002164
+
Hg19::chr3:55002193..55002225,+p@chr3:55002193..55002225
+
Hg19::chr3:55002230..55002244,+p@chr3:55002230..55002244
+
Hg19::chr5:179720177..179720223,+p1@ENST00000504573
Hg19::chr5:179757790..179757847,-p2@GFPT2
Hg19::chr5:179757851..179757870,-p4@GFPT2
Hg19::chr5:179757923..179757948,-p3@GFPT2
Hg19::chr5:81683619..81683623,+p@chr5:81683619..81683623
+
Hg19::chr6:137314390..137314394,-p1@ENST00000418699
p1@ENST00000432330
Hg19::chr6:139013065..139013100,+p6@FLJ46906
Hg19::chr6:73785930..73785949,-p@chr6:73785930..73785949
-
Hg19::chr6:73786593..73786601,+p@chr6:73786593..73786601
+
Hg19::chr6:73786620..73786627,+p@chr6:73786620..73786627
+
Hg19::chr7:40832998..40833012,+p3@C7orf10
Hg19::chr7:40833016..40833066,+p2@C7orf10
Hg19::chr7:43733671..43733688,-p@chr7:43733671..43733688
-
Hg19::chr7:63539651..63539654,+p1@ENST00000430271
Hg19::chr8:123580859..123580902,-p@chr8:123580859..123580902
-
Hg19::chr8:123580905..123580931,-p@chr8:123580905..123580931
-
Hg19::chr8:123580943..123580958,-p@chr8:123580943..123580958
-
Hg19::chr8:123580969..123580991,-p@chr8:123580969..123580991
-
Hg19::chr8:123580995..123581003,-p@chr8:123580995..123581003
-
Hg19::chr8:123581008..123581037,-p@chr8:123581008..123581037
-
Hg19::chr8:32579421..32579432,+p26@NRG1
Hg19::chr8:94870047..94870056,+p30@PDP1
Hg19::chr9:119051028..119051054,-p1@ENST00000438048
Hg19::chr9:140350189..140350212,-p30@NELF
Hg19::chr9:140351903..140351920,-p6@NELF
Hg19::chrX:29686367..29686386,+p@chrX:29686367..29686386
+


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:0019887protein kinase regulator activity0.0272063216252323
GO:0051302regulation of cell division0.0272063216252323
GO:0004360glutamine-fructose-6-phosphate transaminase (isomerizing) activity0.0272063216252323
GO:0019207kinase regulator activity0.0272063216252323
GO:0030297transmembrane receptor protein tyrosine kinase activator activity0.0292212530700774
GO:0030971receptor tyrosine kinase binding0.0292212530700774
GO:0006002fructose 6-phosphate metabolic process0.0292212530700774
GO:0030296protein tyrosine kinase activator activity0.0383416067561451
GO:0005031tumor necrosis factor receptor activity0.0454285307791918
GO:0043120tumor necrosis factor binding0.0459896188608919
GO:0005035death receptor activity0.0464473247508643
GO:0016538cyclin-dependent protein kinase regulator activity0.0468274943289149
GO:0030295protein kinase activator activity0.0471480208963674



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>

Uber Anatomy
Ontology termp-valuen
bronchoalveolar duct junction1.55e-982
alveolar duct1.55e-982
bronchiole1.55e-982
pulmonary alveolus epithelium2.39e-663
alveolus2.39e-663
pulmonary lobule2.39e-663
lobule2.39e-663
alveolus of lung2.39e-663
alveolar system2.39e-663
pulmonary acinus2.39e-663
alveolar sac2.39e-663
alveolar wall2.39e-663
anatomical wall6.76e-1812
tracheobronchial tree1.22e-1415
lower respiratory tract1.22e-1415
duct6.95e-1219
respiratory tract epithelium6.95e-1219
lung epithelium6.95e-1219
lung1.80e-1022
simple squamous epithelium1.80e-1022
respiratory tube1.80e-1022
respiration organ1.80e-1022
pair of lungs1.80e-1022
lung primordium1.80e-1022
lung bud1.80e-1022
epithelial sac2.15e-0925
squamous epithelium2.15e-0925
sac4.34e-0926
respiratory system epithelium1.52e-0828
thoracic cavity element2.74e-0734
thoracic cavity2.74e-0734
thoracic segment organ4.03e-0735
epithelial bud8.21e-0737
Disease
Ontology termp-valuen
lung adenocarcinoma1.55e-982
non-small cell lung carcinoma1.48e-405
bronchus cancer1.78e-297
bronchogenic carcinoma1.78e-297
lung carcinoma2.62e-239
lung cancer1.22e-1415
respiratory system cancer8.02e-1416


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
JUN#3725163.080081031959713.99486758543661e-050.000741988219376515
STAT3#6774193.07492053762976.20075441492697e-060.000183196772373567
TCF7L2#6934193.148205456917074.39975432367538e-060.000137782891097551



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

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