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Coexpression cluster:C2509: Difference between revisions

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|full_id=C2509_adipose_heart_lung_Renal_Endothelial_CD4_Hepatic
|full_id=C2509_adipose_heart_lung_Renal_Endothelial_CD4_Hepatic
|id=C2509
|id=C2509
|ontology_enrichment_celltype=CL:0000115!5.42e-18!35;CL:0002139!1.36e-16!24;CL:0000071!1.07e-12!18;CL:0002546!1.07e-12!18;CL:0002078!1.59e-12!44;CL:0000542!4.51e-10!53;CL:0000051!4.51e-10!53;CL:0000838!4.93e-10!52;CL:0000213!2.66e-09!57;CL:0000215!2.66e-09!57;CL:0000084!9.54e-09!25;CL:0000827!9.54e-09!25;CL:0000791!1.44e-08!18;CL:0000789!1.44e-08!18;CL:0002420!1.44e-08!18;CL:0002419!1.44e-08!18;CL:0000790!1.44e-08!18;CL:1000413!2.91e-07!9;CL:0000222!5.09e-07!119;CL:0000625!5.23e-07!11
|ontology_enrichment_celltype=CL:0000115!7.86e-19!36;CL:0002139!1.16e-16!24;CL:0002078!4.53e-13!45;CL:0000071!8.96e-13!18;CL:0002546!8.96e-13!18;CL:0000213!6.11e-10!58;CL:0000215!6.11e-10!58;CL:0000542!3.26e-09!53;CL:0000051!3.26e-09!53;CL:0000838!3.74e-09!52;CL:0002242!1.71e-08!55;CL:0000791!8.11e-08!18;CL:0000789!8.11e-08!18;CL:0002420!8.11e-08!18;CL:0002419!8.11e-08!18;CL:0000790!8.11e-08!18;CL:0000084!8.25e-08!25;CL:0000827!8.25e-08!25;CL:0000222!9.68e-08!121;CL:1000413!2.35e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.06e-34!115;UBERON:0001009!1.99e-18!113;UBERON:0004535!4.41e-17!110;UBERON:0001049!7.65e-14!57;UBERON:0005068!7.65e-14!57;UBERON:0006241!7.65e-14!57;UBERON:0007135!7.65e-14!57;UBERON:0000055!7.66e-14!69;UBERON:0000025!7.46e-13!194;UBERON:0001986!1.07e-12!18;UBERON:0004638!1.07e-12!18;UBERON:0004852!1.07e-12!18;UBERON:0003075!1.55e-12!86;UBERON:0007284!1.55e-12!86;UBERON:0002049!4.18e-12!79;UBERON:0007798!4.18e-12!79;UBERON:0004872!4.40e-12!84;UBERON:0004111!5.25e-12!241;UBERON:0002616!7.48e-12!59;UBERON:0001981!6.12e-11!60;UBERON:0007500!6.12e-11!60;UBERON:0004537!6.12e-11!60;UBERON:0006965!6.12e-11!60;UBERON:0003080!6.96e-11!42;UBERON:0002346!2.32e-10!90;UBERON:0002780!2.41e-10!41;UBERON:0001890!2.41e-10!41;UBERON:0006240!2.41e-10!41;UBERON:0000487!3.87e-10!22;UBERON:0000477!8.69e-10!286;UBERON:0002020!1.62e-09!34;UBERON:0003528!1.62e-09!34;UBERON:0005743!2.36e-09!86;UBERON:0001017!2.46e-09!82;UBERON:0000955!4.77e-09!69;UBERON:0006238!4.77e-09!69;UBERON:0001893!4.82e-09!34;UBERON:0002791!8.37e-09!33;UBERON:0001869!1.41e-08!32;UBERON:0000073!1.62e-08!94;UBERON:0001016!1.62e-08!94;UBERON:0003056!6.22e-08!61;UBERON:0006914!8.48e-08!25;UBERON:0002619!1.03e-07!22;UBERON:0003915!2.91e-07!9;UBERON:0004700!2.91e-07!9;UBERON:0001917!2.91e-07!9;UBERON:0001950!7.16e-07!20
|ontology_enrichment_uberon=UBERON:0007023!4.77e-34!114;UBERON:0001009!2.06e-18!112;UBERON:0004535!3.99e-17!109;UBERON:0001049!2.17e-14!56;UBERON:0005068!2.17e-14!56;UBERON:0006241!2.17e-14!56;UBERON:0007135!2.17e-14!56;UBERON:0000055!3.53e-14!68;UBERON:0000073!1.90e-13!53;UBERON:0002616!1.90e-13!53;UBERON:0000025!5.15e-13!192;UBERON:0004638!8.96e-13!18;UBERON:0001986!8.96e-13!18;UBERON:0004852!8.96e-13!18;UBERON:0004872!1.53e-12!83;UBERON:0002049!2.18e-12!78;UBERON:0007798!2.18e-12!78;UBERON:0003075!3.81e-12!82;UBERON:0007284!3.81e-12!82;UBERON:0004111!6.65e-12!240;UBERON:0007500!2.35e-11!59;UBERON:0001981!2.35e-11!59;UBERON:0004537!2.35e-11!59;UBERON:0006965!2.35e-11!59;UBERON:0002780!5.16e-11!41;UBERON:0001890!5.16e-11!41;UBERON:0003080!5.16e-11!41;UBERON:0006240!5.16e-11!41;UBERON:0010314!7.77e-11!132;UBERON:0000487!2.67e-10!22;UBERON:0001017!3.62e-10!81;UBERON:0003528!3.90e-10!34;UBERON:0002020!3.90e-10!34;UBERON:0002346!4.98e-10!86;UBERON:0001893!1.34e-09!34;UBERON:0001016!2.54e-09!89;UBERON:0000955!2.75e-09!68;UBERON:0006238!2.75e-09!68;UBERON:0002791!3.76e-09!32;UBERON:0001869!3.97e-09!32;UBERON:0002619!3.97e-08!22;UBERON:0003056!5.38e-08!61;UBERON:0006914!7.47e-08!25;UBERON:0003081!8.91e-08!203;UBERON:0000477!2.10e-07!373;UBERON:0003915!2.35e-07!9;UBERON:0004700!2.35e-07!9;UBERON:0001917!2.35e-07!9;UBERON:0001950!3.19e-07!20;UBERON:0010371!3.59e-07!104
|tf_chipseq_enrich=ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160910738343866!FOS#2353;4:8.9979553088944:0.000152514771116863:0.0019486775361725!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443935964908439!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.0012941160647643!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322297292558593!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244280340310132!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248936788613254
|tf_chipseq_enrich=ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160910738343866!FOS#2353;4:8.9979553088944:0.000152514771116863:0.0019486775361725!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443935964908439!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.0012941160647643!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322297292558593!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244280340310132!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248936788613254
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18999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.00545181,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0230803,0.187953,0.051459,0.114868,0.0027083,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.00808856,0.00856472,0.173134,0.101893,0.142875,0.167635,0.171311,0.0721023,0.00885745,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.0705088,0.107849,0.0150607,0.278645,0.365775,0.155708,0.248017,0.22995,0.285695,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.00455803,0.286748,0.367925,0.0471607,0.163865,0.226359,7.74729e-06,0.881117,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.0127656,0.110256,0.00226167,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.00777449,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.154895,0.140541,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.00640224,0.459091,0.00888122,0.502211,0.296013,0.0221603,0.537932,0.459994,0.00698686,0.548059,0.25423,0.490559,0.45013,0.500698,0.00420596,0.111549,9.48574e-05,0.0074346,7.41116e-05,0.14198,0.0131065,0.603763,0.184287,0.627201,3.52173e-05,0.293249,0.290703,0.622694,1.20073e-07,0.139104,0.00116273,0.608176,0.000842547,0.0021436,0.365494,0.212703,0.0102049,0.364079,0.315494,0.0575699,0.0181617,0.206595,0.328518,0.0458249,0.310552,4.70505e-05,0.483764,5.23163e-08,0.0201581,0.209437,1.6443e-10,1.98155e-06,0.00037168,4.40515e-07,0.464001,5.69321e-05,0.579004,5.52018e-05,5.5579e-07,0.137711,0.261575,0.257956,0.264245,0.00147206,0.326516,0.0391986,0.436016,0.00431716,0.202522,0.183837,0.00598078,0.126097,0.3955,3.35653e-05,0.212239,0.294954,0.156999,0.35974,0.667777,0.0912179,0.234254,0.357409,2.30198e-07,0.365184,0.50338,0.620526,0.404625,0.0563812,0.424691,0.132999,0.479581,0.259048,0.172925,0.00410246,0.284496,0.512545,0.512178,0.563206,2.64616e-06,0.00663196,0.263302,0.192292,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.00349006,0.503881,0.454761,0.639483,0.0295677,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.155207,0.385425,0.0531591,0.461541,0.386339,0.382854,0.0650585,0.478745,0.00289554,0.00716065,0.475047,0.557967,0.00277992,0.0442299,0.000452027,0.2536,0.246827,0.564333,7.07534e-07,0.387134,0.198743,0.358813,0.100705,0.0554837,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.119749,0.42505,0.254628,0.00183295,0.479347,0.416962,0.632833,0.378333,0.0120675,0.0384092,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.0331645,0.211271,0.281295,0.0394002,0.118257,0.125087,0.215123,0.321224,0.00407337,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.0140903,0.279553,0.25563,0.0316941,0.160955,0.000254771,0.0432189,0.122439,0.16188,0.0293669,0.290415,0.353147,0.112422,0.170886,0.00399713,0.315656,0.284866,0.0887542,0.0395756,0.338547,0.147872,0.189388,0.293546,0.210125,0.00536668,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.00774558,0.195748,0.00454462,0.0138433,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.000140205,0.25788,0.181895,0.253768,0.0528669,0.202977,0.170837,0.327002,0.28543,0.222656,0.00015342,0.127111,0.259989,0.390754,0.355805,0.0433915,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.032013,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.362662,0.433518,0.184359,0.334474,0.325785,0.0364266,0.291176,0.376537,0.0588457,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.0163014,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.0729297,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.000365823,0.11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}}
}}

Revision as of 14:06, 19 October 2012


Full id: C2509_adipose_heart_lung_Renal_Endothelial_CD4_Hepatic



Phase1 CAGE Peaks

Hg19::chr1:101702417..101702481,+p1@S1PR1
Hg19::chr1:101702482..101702493,+p6@S1PR1
Hg19::chr1:101702501..101702512,+p5@S1PR1
Hg19::chr1:101702564..101702584,+p2@S1PR1


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

No GOStat results

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
adult organism4.77e-34114
circulatory system2.06e-18112
cardiovascular system3.99e-17109
neural tube2.17e-1456
neural rod2.17e-1456
future spinal cord2.17e-1456
neural keel2.17e-1456
vessel3.53e-1468
regional part of nervous system1.90e-1353
regional part of brain1.90e-1353
tube5.15e-13192
blood vessel endothelium8.96e-1318
endothelium8.96e-1318
cardiovascular system endothelium8.96e-1318
splanchnic layer of lateral plate mesoderm1.53e-1283
vasculature2.18e-1278
vascular system2.18e-1278
neural plate3.81e-1282
presumptive neural plate3.81e-1282
anatomical conduit6.65e-12240
epithelial tube open at both ends2.35e-1159
blood vessel2.35e-1159
blood vasculature2.35e-1159
vascular cord2.35e-1159
regional part of forebrain5.16e-1141
forebrain5.16e-1141
anterior neural tube5.16e-1141
future forebrain5.16e-1141
structure with developmental contribution from neural crest7.77e-11132
simple squamous epithelium2.67e-1022
central nervous system3.62e-1081
brain grey matter3.90e-1034
gray matter3.90e-1034
neurectoderm4.98e-1086
telencephalon1.34e-0934
nervous system2.54e-0989
brain2.75e-0968
future brain2.75e-0968
regional part of telencephalon3.76e-0932
cerebral hemisphere3.97e-0932
regional part of cerebral cortex3.97e-0822
pre-chordal neural plate5.38e-0861
squamous epithelium7.47e-0825
lateral plate mesoderm8.91e-08203
anatomical cluster2.10e-07373
endothelial tube2.35e-079
arterial system endothelium2.35e-079
endothelium of artery2.35e-079
neocortex3.19e-0720
ecto-epithelium3.59e-07104


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
ELF1#199744.258097958807540.003041525565781240.0160910738343866
FOS#235348.99795530889440.0001525147711168630.0019486775361725
PAX5#507946.669565531177830.0005052774169483260.00443935964908439
RAD21#5885410.35503389545638.6948481184721e-050.0012941160647643
TAF1#687243.343046285745290.008005664898701650.0322297292558593
TBP#690843.706770687096390.005296377814784350.0244280340310132
ZNF263#1012748.221841637010680.0002187871180958320.00248936788613254



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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