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Coexpression cluster:C2914: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.26e-18!115;UBERON:0001474!1.57e-17!86;UBERON:0002371!4.76e-17!80;UBERON:0004765!6.58e-17!101;UBERON:0001434!6.58e-17!101;UBERON:0001049!5.17e-15!57;UBERON:0005068!5.17e-15!57;UBERON:0006241!5.17e-15!57;UBERON:0007135!5.17e-15!57;UBERON:0002390!4.14e-14!102;UBERON:0003061!4.14e-14!102;UBERON:0003080!2.92e-13!42;UBERON:0002616!7.71e-13!59;UBERON:0002780!1.04e-12!41;UBERON:0001890!1.04e-12!41;UBERON:0006240!1.04e-12!41;UBERON:0001017!1.36e-10!82;UBERON:0002020!2.02e-10!34;UBERON:0003528!2.02e-10!34;UBERON:0002193!2.22e-10!112;UBERON:0000062!3.39e-10!511;UBERON:0000955!3.91e-10!69;UBERON:0006238!3.91e-10!69;UBERON:0001893!7.70e-10!34;UBERON:0002791!8.13e-10!33;UBERON:0005743!1.56e-09!86;UBERON:0001869!3.01e-09!32;UBERON:0002204!4.33e-09!167;UBERON:0000073!6.10e-09!94;UBERON:0001016!6.10e-09!94;UBERON:0003075!1.08e-07!86;UBERON:0007284!1.08e-07!86;UBERON:0000153!3.12e-07!129;UBERON:0007811!3.12e-07!129;UBERON:0000033!4.75e-07!123;UBERON:0000956!5.95e-07!25;UBERON:0000203!5.95e-07!25;UBERON:0002619!7.07e-07!22
|ontology_enrichment_uberon=UBERON:0007023!3.26e-18!115;UBERON:0001474!1.57e-17!86;UBERON:0002371!4.76e-17!80;UBERON:0004765!6.58e-17!101;UBERON:0001434!6.58e-17!101;UBERON:0001049!5.17e-15!57;UBERON:0005068!5.17e-15!57;UBERON:0006241!5.17e-15!57;UBERON:0007135!5.17e-15!57;UBERON:0002390!4.14e-14!102;UBERON:0003061!4.14e-14!102;UBERON:0003080!2.92e-13!42;UBERON:0002616!7.71e-13!59;UBERON:0002780!1.04e-12!41;UBERON:0001890!1.04e-12!41;UBERON:0006240!1.04e-12!41;UBERON:0001017!1.36e-10!82;UBERON:0002020!2.02e-10!34;UBERON:0003528!2.02e-10!34;UBERON:0002193!2.22e-10!112;UBERON:0000062!3.39e-10!511;UBERON:0000955!3.91e-10!69;UBERON:0006238!3.91e-10!69;UBERON:0001893!7.70e-10!34;UBERON:0002791!8.13e-10!33;UBERON:0005743!1.56e-09!86;UBERON:0001869!3.01e-09!32;UBERON:0002204!4.33e-09!167;UBERON:0000073!6.10e-09!94;UBERON:0001016!6.10e-09!94;UBERON:0003075!1.08e-07!86;UBERON:0007284!1.08e-07!86;UBERON:0000153!3.12e-07!129;UBERON:0007811!3.12e-07!129;UBERON:0000033!4.75e-07!123;UBERON:0000956!5.95e-07!25;UBERON:0000203!5.95e-07!25;UBERON:0002619!7.07e-07!22
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513796194962499!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268791576930386!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820197202136417!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106819631573628!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000615285551800627!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724959123821004!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.79645281630527e-05!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186667496785775!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000745442396696081!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392712657766967!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032340681404692!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024511383994251
|tfbs_overrepresentation=0.0196021,0.0774498,0.090627,0.0631091,0.257053,0.363996,0.0569281,0.510252,1.55673e-07,0.000589049,0.181435,0.000427152,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.000527157,0.243245,0.172742,0.000226999,0.124486,0.0550418,0.000353185,0.268949,0.00739132,0.186914,0.122514,0.0382352,0.149094,0.0239693,0.0394878,0.0877018,0.111013,1.29234e-09,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.00156695,0.0715789,0.0924421,0.12203,0.255843,0.00131748,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,6.60031e-05,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.470097,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.0083674,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.0780785,0.320801,0.0848546,0.268505,0.355976,0.0827752,0.112676,0.0655645,0.12511,0.00200553,0.112199,0.150351,0.690341,0.199405,0.121709,0.0689843,0.0759036,0.350158,0.184542,0.0491142,0.000378855,0.0541957,0.0883058,0.0184799,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.000347773,0.182323,0.112709,0.134107,0.000153866,0.119051,0.0196757,0.110868,0.175735,0.078637,0.00502016,7.61872e-05,0.0302655,0.164103,0.141472,0.085537,0.0027388,0.0438087,0.0052702,0.0302521,0.166414,0.0378473,0.0016282,0.00801724,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.0124479,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.00143091,0.0146311,0.0534404,0.392741,0.2321,0.179282,0.052046,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,6.53082e-07,0.117261,0.0797088,0.0408965,0.00328703,0.01681,0.329956,0.346995,0.197158,0.265132,0.0288641,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.0252658,0.202467,0.208718,0.0972471,0.0144563,0.180711,7.81501e-06,0.0797807,0.0790532,0.675167,0.137848,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.0242127,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.00596033,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.000267906,0.0916845,0.0307561,0.0816983,0.0278083,0.211672,0.000887749,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,9.04626e-05,0.00358623,0.0594434,0.0458938,0.113754,0.0504034,0.169684,0.690367,0.00167214,0.0560372,0.0122628,0.100371,0.0854389,0.000462571,0.420045,0.73391,0.332539,0.186966,0.464128,0.389374,0.594055,0.414547,0.489273,0.413223,0.639461,0.364388,0.34505,0.369161,0.500422,0.49089,0.0305759,0.00026689,0.241524,0.45167,0.234628,0.520726,0.143893,0.101233,0.00037332,0.170724,0.467825,0.563725,0.164225,0.632838,0.624969,0.127765,0.00622965,0.00216594,0.322903,0.350886,0.380582,0.218919,0.398372,0.286293,0.239547,0.34907,0.0105546,0.395864,0.683133,0.0782875,0.547291,0.317802,0.512763,0.369971,0.214221,0.537928,0.464342,0.0295245,0.0384361,0.0301914,0.0255809,5.44744e-06,3.77863e-06,0.0696107,0.302142,0.239545,0.432689,0.272581,0.067384,0.145459,0.239383,0.250139,0.626346,0.316925,0.0728506,0.573659,0.211506,0.0883859,0.0962508,0.238465,0.70198,0.128535,0.6873,0.508325,0.773224,0.651927,0.656755,0.188468,0.00464429,0.0144019,0.794849,0.0596868,4.41748e-06,0.293026,0.0537754,0.694744,0.605423,0.0799295,0.429205,0.00197808,0.365653,0.0166186,0.00493387,0.00105075,0.180014,0.525923,1.74965e-06,0.421082,0.25441,0.202782,0.00579711,0.166182,0.584705,0.517001,0.0746589,8.9551e-05,0.419676,0.188259,0.0191441,0.477589,0.131612,0.546448,0.198922,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.074448,0.429696,0.386216,0.385297,0.00845714,0.239407,0.627185,0.360203,0.333725,0.447838,0.289666,0.500627,0.513045,0.452694,0.565545,0.119811,0.265037,0.000575107,0.167853,0.53531,0.341771,0.424526,0.290547,0.356381,0.184395,0.0094773,0.624689,1.76981e-07,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.261511,0.729876,0.111753,0.64428,0.113459,0.576549,0.499072,0.158149,0.00246373,0.397546,0.0919254,0.0735469,0.000219546,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.540322,0.247151,0.146385,0.365815,4.93132e-07,0.382413,0.164977,0.175633,0.139918,0.00937608,0.0828344,0.135364,0.0238089,0.383126,0.354433,0.48311,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,1.92311e-05,0.0580534,0.00518407,0.161297,0.168389,0.00411807,0.249506,0.111145,0.0660736,0.00023483,0.0879235,0.235214,0.145546,0.28124,0.000243828,0.251882,1.45215e-09,0.0323461,0.0637178,0.257309,0.153907,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.00227049,0.183585,0.271662,0.03989,0.171436,0.05892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}}
}}

Revision as of 13:41, 5 September 2012


Full id: C2914_CD14_breast_small_spinal_osteosarcoma_skin_Macrophage



Phase1 CAGE Peaks

Hg19::chr8:116681150..116681164,-p5@TRPS1
Hg19::chr8:116681194..116681214,-p1@TRPS1
Hg19::chr8:116681221..116681236,-p3@TRPS1
Hg19::chr8:116681247..116681261,-p8@TRPS1


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 organism3.26e-18115
bone element1.57e-1786
bone marrow4.76e-1780
skeletal element6.58e-17101
skeletal system6.58e-17101
neural tube5.17e-1557
neural rod5.17e-1557
future spinal cord5.17e-1557
neural keel5.17e-1557
hematopoietic system4.14e-14102
blood island4.14e-14102
anterior neural tube2.92e-1342
regional part of brain7.71e-1359
regional part of forebrain1.04e-1241
forebrain1.04e-1241
future forebrain1.04e-1241
central nervous system1.36e-1082
gray matter2.02e-1034
brain grey matter2.02e-1034
hemolymphoid system2.22e-10112
organ3.39e-10511
brain3.91e-1069
future brain3.91e-1069
telencephalon7.70e-1034
regional part of telencephalon8.13e-1033
cerebral hemisphere3.01e-0932
musculoskeletal system4.33e-09167
regional part of nervous system6.10e-0994
nervous system6.10e-0994
neural plate1.08e-0786
presumptive neural plate1.08e-0786
anterior region of body3.12e-07129
craniocervical region3.12e-07129
head4.75e-07123
cerebral cortex5.95e-0725
pallium5.95e-0725
regional part of cerebral cortex7.07e-0722


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
CCNT2#90546.336201576962630.0006203100587215640.00513796194962499
CEBPB#105147.971147625824820.0002476385788090830.00268791576930386
CTCF#1066445.360256373075030.001211145381643620.00820197202136417
E2F1#186944.907389214879320.001724022357361790.0106819631573628
GATA1#2623413.56030814380042.95627390049268e-050.000615285551800627
GATA2#2624412.7449317335543.78864877853583e-050.000724959123821004
GATA3#2625427.2365163572061.81561517799785e-066.79645281630527e-05
HEY1#2346244.040111043105710.00375304636917980.0186667496785775
JUN#3725412.51282919233634.07770316866756e-050.000745442396696081
JUND#372746.994663941871030.000417684217818580.00392712657766967
TAF1#687243.343046285745290.008005664898701650.032340681404692
TBP#690843.706770687096390.005296377814784350.024511383994251



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.