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Coexpression cluster:C514: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0006954!inflammatory response!0.00647906594947299!8605;8767;6401$GO:0009611!response to wounding!0.00983701397986704!8605;8767;6401$GO:0008903!hydroxypyruvate isomerase activity!0.0127385733489111!81888$GO:0006952!defense response!0.0127385733489111!8605;8767;6401$GO:0009605!response to external stimulus!0.0129117202217266!8605;8767;6401$GO:0046475!glycerophospholipid catabolic process!0.0150696823597155!8605$GO:0047499!calcium-independent phospholipase A2 activity!0.0193733097010132!8605$GO:0019369!arachidonic acid metabolic process!0.022599866037022!8605$GO:0050700!CARD domain binding!0.0271142515575275!8767$GO:0030274!LIM domain binding!0.0271142515575275!8767$GO:0007567!parturition!0.0328589881048493!8605$GO:0006950!response to stress!0.0363166120593536!8605;8767;6401$GO:0009395!phospholipid catabolic process!0.045157841689947!8605$GO:0042809!vitamin D receptor binding!0.048153480631656!9862$GO:0016455!RNA polymerase II transcription mediator activity!0.048153480631656!9862
|gostat_on_coexpression_clusters=GO:0006954!inflammatory response!0.00647906594947299!8605;8767;6401$GO:0009611!response to wounding!0.00983701397986704!8605;8767;6401$GO:0008903!hydroxypyruvate isomerase activity!0.0127385733489111!81888$GO:0006952!defense response!0.0127385733489111!8605;8767;6401$GO:0009605!response to external stimulus!0.0129117202217266!8605;8767;6401$GO:0046475!glycerophospholipid catabolic process!0.0150696823597155!8605$GO:0047499!calcium-independent phospholipase A2 activity!0.0193733097010132!8605$GO:0019369!arachidonic acid metabolic process!0.022599866037022!8605$GO:0050700!CARD domain binding!0.0271142515575275!8767$GO:0030274!LIM domain binding!0.0271142515575275!8767$GO:0007567!parturition!0.0328589881048493!8605$GO:0006950!response to stress!0.0363166120593536!8605;8767;6401$GO:0009395!phospholipid catabolic process!0.045157841689947!8605$GO:0042809!vitamin D receptor binding!0.048153480631656!9862$GO:0016455!RNA polymerase II transcription mediator activity!0.048153480631656!9862
|id=C514
|id=C514
|ontology_enrichment_celltype=CL:0000115!3.11e-13!35;CL:0002139!2.17e-12!24;CL:0002078!5.92e-12!44;CL:0000213!1.03e-09!57;CL:0000215!1.03e-09!57;CL:0000071!1.61e-08!18;CL:0002546!1.61e-08!18
|ontology_enrichment_celltype=CL:0002139!2.42e-53!24;CL:0005020!1.64e-41!6;CL:0002138!1.64e-41!6;CL:0005022!1.64e-41!6;CL:0000115!6.18e-40!36;CL:0002078!2.35e-31!45;CL:0000213!1.17e-23!58;CL:0000215!1.17e-23!58;CL:0000071!4.49e-23!18;CL:0002546!4.49e-23!18;CL:0002144!1.05e-21!3;CL:0000222!8.69e-10!121;CL:0002618!9.81e-10!3;CL:1000413!2.53e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!2.88e-21!241;UBERON:0007023!1.73e-18!115;UBERON:0000025!2.53e-18!194;UBERON:0000477!6.14e-18!286;UBERON:0000480!1.59e-17!626;UBERON:0000467!3.25e-17!625;UBERON:0000468!7.40e-17!659;UBERON:0000055!1.30e-15!69;UBERON:0003914!2.56e-15!118;UBERON:0000922!8.58e-15!612;UBERON:0002050!2.65e-13!605;UBERON:0005423!2.65e-13!605;UBERON:0000923!3.22e-13!604;UBERON:0005291!3.22e-13!604;UBERON:0006598!3.22e-13!604;UBERON:0002532!3.22e-13!604;UBERON:0002049!9.08e-13!79;UBERON:0007798!9.08e-13!79;UBERON:0001981!5.06e-12!60;UBERON:0007500!5.06e-12!60;UBERON:0004537!5.06e-12!60;UBERON:0006965!5.06e-12!60;UBERON:0001009!2.80e-11!113;UBERON:0000483!4.04e-11!309;UBERON:0000119!7.11e-11!312;UBERON:0004872!1.45e-10!84;UBERON:0004535!1.64e-10!110;UBERON:0000481!5.03e-09!347;UBERON:0001986!1.61e-08!18;UBERON:0004638!1.61e-08!18;UBERON:0004852!1.61e-08!18;UBERON:0005177!3.07e-08!107;UBERON:0005172!7.71e-08!55;UBERON:0005173!7.71e-08!55;UBERON:0000926!9.32e-08!448;UBERON:0004120!9.32e-08!448;UBERON:0006603!9.32e-08!448;UBERON:0001637!1.21e-07!42;UBERON:0003509!1.21e-07!42;UBERON:0004572!1.21e-07!42;UBERON:0003081!1.38e-07!216;UBERON:0000490!1.86e-07!138;UBERON:0000062!5.46e-07!511
|ontology_enrichment_uberon=UBERON:0002465!4.09e-33!10;UBERON:0001473!4.97e-31!8;UBERON:0004536!4.97e-31!8;UBERON:0006558!4.97e-31!8;UBERON:0004638!4.49e-23!18;UBERON:0001986!4.49e-23!18;UBERON:0004852!4.49e-23!18;UBERON:0010523!1.05e-21!3;UBERON:0001915!1.05e-21!3;UBERON:0001982!1.05e-21!3;UBERON:0000055!1.22e-19!68;UBERON:0000487!1.12e-18!22;UBERON:0002049!9.72e-17!78;UBERON:0007798!9.72e-17!78;UBERON:0006914!2.67e-16!25;UBERON:0004535!8.43e-13!109;UBERON:0001009!2.26e-12!112;UBERON:0004111!2.72e-08!240;UBERON:0001301!4.40e-08!1;UBERON:0007500!7.49e-08!59;UBERON:0001981!7.49e-08!59;UBERON:0004537!7.49e-08!59;UBERON:0006965!7.49e-08!59;UBERON:0002372!7.59e-08!1;UBERON:0001961!7.59e-08!1;UBERON:0001744!7.59e-08!1;UBERON:0001735!7.59e-08!1;UBERON:0004872!8.08e-08!83;UBERON:0003915!2.53e-07!9;UBERON:0004700!2.53e-07!9;UBERON:0001917!2.53e-07!9;UBERON:0000477!2.54e-07!373;UBERON:0001638!4.62e-07!9;UBERON:0003920!4.62e-07!9;UBERON:0004582!4.62e-07!9
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0.937727,0.182735,0.923711,0.437934,0.214645,0.308574,0.96164,0.185435,0.499229,0.503087,0.837701,0.159801,0.855787,0.608154,0.211589,0.422522,0.287944,0.0684644,0.827216,0.769674,0.71767,0.569618,0.950507,0.00647042,0.601932,0.378155,0.678903,0.401036,0.701952,0.701934,0.616682,0.599545,0.666548,0.597186,0.428223,0.650953,0.868739,0.252299,0.450163,0.471628,0.574933,0.38344,0.500313,0.562062,0.207683,0.824805,0.871698,0.2734,0.466429,0.265077,0.318145,0.37568,0.445667,0.606798,0.187529,0.370266,0.857275,0.959742,0.880379,0.77003,0.871147,0.533106,0.367032,0.328626,0.853873,0.299365,0.253653,0.575713,0.0554438,0.685432,0.882952,0.358506,0.781428,0.611135,0.195384,0.553066,0.684915,0.996154,0.997156,0.0523218,0.434406,0.497219,0.341862,0.498808,0.262149,0.453683,0.748926,0.375958,0.244499,0.503741,0.354161,0.785282,0.264113,0.205881,0.574149,0.241402,0.282895,0.517064,0.117111,0.313959,0.485849,0.443324,0.297565,0.475641,0.377588,0.868466,0.629121,0.727751,0.771789,0.474226,0.686443,0.680044,0.918047,0.259237,0.321823,0.720352,0.619039,0.922915,0.270253,0.360861,0.439211,0.311174,0.240361,0.624525,0.459217,0.636046,0.673757,0.725128,0.587519,0.788546,0.518411,0.869824,0.532516,0.408856,0.694998,0.513464,0.511834,0.710464,0.684185,0.450032,0.548898,0.247666,0.596934,0.132099,0.533339,0.481419,0.513212,0.143867,0.668089,0.434597,0.607878,0.299539,0.714737,0.399122,0.126424,0.639215,0.655662,0.928256,0.306133,0.818177,0.692392,0.434502,0.467462,0.95664,0.830433,0.197893,0.217267,0.569631,0.234019,0.213124,0.408418,0.762941,0.152663,0.956678,0.793917,0.849875,0.969013,0.937512,0.647168,0.47923,0.73287,0.360605,0.749763,0.60432,0.32559,0.59577,0.0511149,0.128723,0.778098,0.345908,0.374609,0.785204,0.277038,0.0375518,0.985372,0.998183,0.786829,0.813205,0.516988,0.790362,0.325947,0.7919,0.859061,0.890661,0.336066,0.292238,0.719117,0.603933,0.147171,0.0186009,0.914508,0.524813,0.534841,0.474026,0.81239,0.945472,0.797142,0.9566,0.967982,0.2854,0.838445,0.742029,0.777777,0.96297,0.532048,0.952175,0.979618,0.895394,0.715637,0.976741,0.395872,0.738824,0.401542,0.0666169,0.105327,0.42636,0.475853,0.0741873,0.0837084,0.599138,0.617077,0.454764,0.0281369,0.738178,0.291265,0.0222088,0.53631,0.144045,0.129101,0.0281331,0.120745,0.59131,0.685935,0.978493,0.822121,0.6336,0.903047,0.881414,0.107201,0.815194,0.1746,0.455797,0.996524,0.839968,0.192775,0.833119,0.224772,0.318062,0.897938,0.761531,0.747185,0.699648,0.592235,0.902164,0.665676,0.733561,0.406909,0.197158,0.903239,0.685157,0.697834,0.769973,0.936316,0.957328,0.756623,0.485072,0.948924,0.138243,0.220581,0.158124,0.300672,0.773576,0.869307,0.480201,0.305027,0.568265,0.643159,0.809016,0.304881,0.888909,0.638534,0.0579344,0.337497,0.42113,0.251727,0.028717,0.500337,0.41322,0.439676,0.258139,0.731853,0.1373,0.513945,0.475528,0.378156,0.31164,0.593981,0.555107,0.737912,0.366352,0.852701,0.519534,0.304449,0.787448,0.900811,0.74594,0.453781,0.3811,0.491838,0.791245,0.697555,0.939335,0.882237,0.0864749,0.401103,0.112876,0.385297,0.5789,0.748102,0.185981,0.359588,0.536372,0.355893,0.360982,0.84219,0.655096,0.0403555,0.289237,0.187739,0.166324,0.432404,0.451923,0.297317,0.825108,0.942293,0.261462,0.752316,0.869953,0.694683,0.725021,0.441414,0.446753,0.918601,0.385919,0.771331,0.383232,0.710818,0.546023,0.000471427,0.180297,0.444418,0.548272,0.695747,0.456739,0.859193,0.415306,0.569708,0.408845,0.0942128,0.778821,0.341797,0.754074,0.844316,0.513289,0.243962,0.790648,0.0046918,0.462069,0.670089,0.20985,0.336557,0.275056,0.244013,0.559946,0.740991,0.478774,0.267954,0.536216,0.463842,0.497844,0.308198,0.767657,0.644868,0.189454,0.728313,0.548777,0.270356,0.890124,0.697339,0.648411,0.832157,0.624798,0.183311,0.18897,0.125402,0.70767,0.362671,0.83378,0.54332,0.745202,0.763881,0.752371,0.600675,0.723852,0.512602,0.522696,0.782599,0.816404,0.680147,0.738704,0.594826,0.146875,0.808026,0.639739,0.569592,0.531803,0.779605,0.678071,0.113491,0.457605,0.742029,0.186559,0.58825,0.771596,0.402439,0.741891,0.491991,0.281488,0.282255,0.625848,0.385757,0.220774,0.282081,0.901064,0.838076,0.759361,0.354484,0.797398,0.716647,0.398723,0.128399,0.328182,0.541619,0.326996,0.48466,0.337521,0.378673,0.56258,0.500235,0.237135,0.340182,0.430665,0.201185,0.216542,0.746375,0.162093,0.330643,0.72428,0.600289,0.278043,0.830335,0.738063,0.787469,0.880698,0.82696,0.690759,0.86487,0.549695,0.208459,0.0898835,0.403268,0.38488,0.868496,0.801858,0.0908675,0.522191,0.771405,0.781357,0.520448,0.727834,0.363115,0.862678,0.593425,0.821957,0.0954589,0.782075,0.118456,0.217442,0.784583,0.165918,0.123461,0.41671,0.898367,0.311997,0.645799,0.295944,0.357633,0.124142,0.472167,0.445648,0.686837,0.641805,0.767256,0.521666,0.162574,0.135783
}}
}}

Revision as of 16:22, 19 October 2012


Full id: C514_Lymphatic_Endothelial_mycosis_appendix_heart_CD14_migratory



Phase1 CAGE Peaks

Hg19::chr12:47053880..47053887,+p@chr12:47053880..47053887
+
Hg19::chr15:89736241..89736275,+p@chr15:89736241..89736275
+
Hg19::chr17:28534879..28534889,-p@chr17:28534879..28534889
-
Hg19::chr17:28534912..28534942,-p@chr17:28534912..28534942
-
Hg19::chr17:38179836..38179841,-p3@MED24
Hg19::chr17:45933057..45933064,-p3@SP6
Hg19::chr17:75873825..75873826,+p@chr17:75873825..75873826
+
Hg19::chr19:48613987..48613999,-p5@PLA2G4C
Hg19::chr1:169703213..169703227,-p1@SELE
Hg19::chr1:43917566..43917577,-p6@HYI
Hg19::chr4:114238344..114238353,+p58@ANK2
Hg19::chr4:38057520..38057536,-p@chr4:38057520..38057536
-
Hg19::chr4:38057595..38057624,-p@chr4:38057595..38057624
-
Hg19::chr4:38057720..38057727,-p@chr4:38057720..38057727
-
Hg19::chr6:29527501..29527515,-p1@UBD
Hg19::chr8:80680913..80680917,-p@chr8:80680913..80680917
-
Hg19::chr8:90769563..90769576,-p1@ENST00000523859
Hg19::chr8:90769801..90769825,+p4@RIPK2


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:0006954inflammatory response0.00647906594947299
GO:0009611response to wounding0.00983701397986704
GO:0008903hydroxypyruvate isomerase activity0.0127385733489111
GO:0006952defense response0.0127385733489111
GO:0009605response to external stimulus0.0129117202217266
GO:0046475glycerophospholipid catabolic process0.0150696823597155
GO:0047499calcium-independent phospholipase A2 activity0.0193733097010132
GO:0019369arachidonic acid metabolic process0.022599866037022
GO:0050700CARD domain binding0.0271142515575275
GO:0030274LIM domain binding0.0271142515575275
GO:0007567parturition0.0328589881048493
GO:0006950response to stress0.0363166120593536
GO:0009395phospholipid catabolic process0.045157841689947
GO:0042809vitamin D receptor binding0.048153480631656
GO:0016455RNA polymerase II transcription mediator activity0.048153480631656



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>


Uber Anatomy
Ontology termp-valuen
lymphoid system4.09e-3310
lymphatic vessel4.97e-318
lymph vasculature4.97e-318
lymphatic part of lymphoid system4.97e-318
blood vessel endothelium4.49e-2318
endothelium4.49e-2318
cardiovascular system endothelium4.49e-2318
microcirculatory vessel1.05e-213
endothelium of capillary1.05e-213
capillary1.05e-213
vessel1.22e-1968
simple squamous epithelium1.12e-1822
vasculature9.72e-1778
vascular system9.72e-1778
squamous epithelium2.67e-1625
cardiovascular system8.43e-13109
circulatory system2.26e-12112
anatomical conduit2.72e-08240
epididymis4.40e-081
epithelial tube open at both ends7.49e-0859
blood vessel7.49e-0859
blood vasculature7.49e-0859
vascular cord7.49e-0859
tonsil7.59e-081
mucosa-associated lymphoid tissue7.59e-081
lymphoid tissue7.59e-081
tonsillar ring7.59e-081
splanchnic layer of lateral plate mesoderm8.08e-0883
endothelial tube2.53e-079
arterial system endothelium2.53e-079
endothelium of artery2.53e-079
anatomical cluster2.54e-07373
vein4.62e-079
venous blood vessel4.62e-079
venous system4.62e-079


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


No analysis results for this cluster

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.