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Coexpression cluster:C3002: Difference between revisions

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|full_id=C3002_Mast_CD34_acute_CD4_Melanocyte_chronic_CD133
|full_id=C3002_Mast_CD34_acute_CD4_Melanocyte_chronic_CD133
|id=C3002
|id=C3002
|ontology_enrichment_celltype=CL:0000791!9.00e-09!18;CL:0000789!9.00e-09!18;CL:0002420!9.00e-09!18;CL:0002419!9.00e-09!18;CL:0000790!9.00e-09!18;CL:0000084!3.80e-08!25;CL:0000827!3.80e-08!25;CL:0000625!4.57e-07!11
|ontology_enrichment_celltype=CL:0000988!1.66e-07!177;CL:0002274!3.22e-07!5;CL:0000457!3.22e-07!5;CL:0002191!3.22e-07!5;CL:0000097!3.22e-07!5;CL:0000831!3.22e-07!5;CL:0002028!3.22e-07!5;CL:0000037!3.99e-07!168;CL:0000566!3.99e-07!168
|ontology_enrichment_disease=DOID:8692!2.76e-09!31;DOID:1240!5.27e-08!39
|ontology_enrichment_disease=DOID:8692!2.52e-11!31;DOID:1240!2.89e-10!39;DOID:2531!6.02e-07!51;DOID:0060083!6.02e-07!51
|ontology_enrichment_uberon=UBERON:0007023!9.61e-30!115;UBERON:0001049!1.45e-14!57;UBERON:0005068!1.45e-14!57;UBERON:0006241!1.45e-14!57;UBERON:0007135!1.45e-14!57;UBERON:0002616!7.74e-13!59;UBERON:0005743!3.20e-12!86;UBERON:0001017!5.73e-12!82;UBERON:0003075!8.96e-12!86;UBERON:0007284!8.96e-12!86;UBERON:0000955!1.19e-11!69;UBERON:0006238!1.19e-11!69;UBERON:0000073!1.83e-10!94;UBERON:0001016!1.83e-10!94;UBERON:0002346!2.83e-10!90;UBERON:0003080!6.05e-10!42;UBERON:0002780!1.72e-09!41;UBERON:0001890!1.72e-09!41;UBERON:0006240!1.72e-09!41;UBERON:0002619!5.68e-08!22;UBERON:0001893!5.81e-08!34;UBERON:0002020!6.04e-08!34;UBERON:0003528!6.04e-08!34;UBERON:0003056!1.19e-07!61;UBERON:0002791!1.44e-07!33;UBERON:0001950!2.34e-07!20;UBERON:0001869!2.93e-07!32;UBERON:0000153!5.12e-07!129;UBERON:0007811!5.12e-07!129;UBERON:0000178!6.21e-07!15;UBERON:0000179!6.21e-07!15;UBERON:0000463!6.21e-07!15;UBERON:0000956!8.88e-07!25;UBERON:0000203!8.88e-07!25
|ontology_enrichment_uberon=UBERON:0007023!2.27e-25!114;UBERON:0000073!4.23e-11!53;UBERON:0002616!4.23e-11!53;UBERON:0001049!1.07e-10!56;UBERON:0005068!1.07e-10!56;UBERON:0006241!1.07e-10!56;UBERON:0007135!1.07e-10!56;UBERON:0000955!1.85e-09!68;UBERON:0006238!1.85e-09!68;UBERON:0000178!2.24e-09!15;UBERON:0000179!2.24e-09!15;UBERON:0000463!2.24e-09!15;UBERON:0003075!9.27e-09!82;UBERON:0007284!9.27e-09!82;UBERON:0002780!1.01e-08!41;UBERON:0001890!1.01e-08!41;UBERON:0003080!1.01e-08!41;UBERON:0006240!1.01e-08!41;UBERON:0001017!5.89e-08!81;UBERON:0001950!6.05e-08!20;UBERON:0001893!6.05e-08!34;UBERON:0002619!6.06e-08!22;UBERON:0003528!7.65e-08!34;UBERON:0002020!7.65e-08!34;UBERON:0002346!7.71e-08!86;UBERON:0001869!3.67e-07!32;UBERON:0002791!4.10e-07!32
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189033293265759!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278137402620999!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0318873522787808!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459780050886568!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000848131440315536!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139547178096867
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189033293265759!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278137402620999!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0318873522787808!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459780050886568!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000848131440315536!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139547178096867
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.00465244,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.00169471,0.114046,0.0180314,0.208242,0.0665252,0.0844722,3.84895e-06,0.0429682,0.00755159,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.0148026,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.00111717,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.00100585,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.0223286,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.782949,0.635872,0.563047,0.823736,0.807281,0.335423,0.0790073,0.261553,0.446302,0.373681,0.309233,0.147559,0.330703,1.05537e-06,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.0582602,0.597171,0.0187414,0.0756284,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.129235,0.647576,0.528324,0.520763,0.370782,0.415647,0.142924,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.0478086,0.476744,0.439556,0.0120909,0.056723,0.608919,0.18237,0.706298,0.513427,0.0133926,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.0583074,0.1002,0.671377,0.188159,0.551561,0.448039,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.294698,0.34331,0.0282052,0.289204,0.327108,0.319027,0.00452305,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.311758,0.335105,0.144809,0.145539,0.385517,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.0391885,0.284629,0.262537,0.359455,0.0277799,0.405955,0.41707,0.363685,0.464871,0.40841,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.552319,0.0439467,0.141758,0.455379,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.0688327,0.539392,0.34988,0.136757,0.404569,0.273024,0.00358327,0.316179,0.0697683,0.0556835,0.192544,0.0779981,3.32302e-05,0.144322,0.223391,0.203656,0.442884,3.31512e-05,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.00817962,0.19559,0.132201,0.0190418,0.0481795,0.00156721,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.000523704,0.00187586,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.000346156,0.09064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}}
}}

Revision as of 14:42, 19 October 2012


Full id: C3002_Mast_CD34_acute_CD4_Melanocyte_chronic_CD133



Phase1 CAGE Peaks

Hg19::chr10:17496557..17496568,-p3@ST8SIA6
Hg19::chr10:17496582..17496601,-p1@ST8SIA6
Hg19::chr10:17496614..17496625,-p5@ST8SIA6


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism2.27e-25114
regional part of nervous system4.23e-1153
regional part of brain4.23e-1153
neural tube1.07e-1056
neural rod1.07e-1056
future spinal cord1.07e-1056
neural keel1.07e-1056
brain1.85e-0968
future brain1.85e-0968
blood2.24e-0915
haemolymphatic fluid2.24e-0915
organism substance2.24e-0915
neural plate9.27e-0982
presumptive neural plate9.27e-0982
regional part of forebrain1.01e-0841
forebrain1.01e-0841
anterior neural tube1.01e-0841
future forebrain1.01e-0841
central nervous system5.89e-0881
neocortex6.05e-0820
telencephalon6.05e-0834
regional part of cerebral cortex6.06e-0822
brain grey matter7.65e-0834
gray matter7.65e-0834
neurectoderm7.71e-0886
cerebral hemisphere3.67e-0732
regional part of telencephalon4.10e-0732
Disease
Ontology termp-valuen
myeloid leukemia2.52e-1131
leukemia2.89e-1039
hematologic cancer6.02e-0751
immune system cancer6.02e-0751


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#90536.336201576962630.003930750035764890.0189033293265759
CTCF#1066435.360256373075030.0064925092527670.0278137402620999
EGR1#195834.988179094810140.008056488137383440.0318873522787808
ELF1#199734.258097958807540.01295179875054610.0459780050886568
GATA3#2625327.2365163572064.94721007899563e-050.000848131440315536
ZBTB7A#5134137.35190930787590.002516255860282270.0139547178096867



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.