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Coexpression cluster:C4327: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.37e-49!115;UBERON:0001049!8.62e-23!57;UBERON:0005068!8.62e-23!57;UBERON:0006241!8.62e-23!57;UBERON:0007135!8.62e-23!57;UBERON:0001017!2.88e-19!82;UBERON:0003080!1.11e-18!42;UBERON:0005743!4.27e-18!86;UBERON:0002780!4.58e-18!41;UBERON:0001890!4.58e-18!41;UBERON:0006240!4.58e-18!41;UBERON:0002616!1.93e-17!59;UBERON:0000073!1.12e-16!94;UBERON:0001016!1.12e-16!94;UBERON:0000955!2.12e-15!69;UBERON:0006238!2.12e-15!69;UBERON:0001893!2.25e-15!34;UBERON:0002020!3.81e-15!34;UBERON:0003528!3.81e-15!34;UBERON:0002791!7.53e-15!33;UBERON:0001869!1.43e-14!32;UBERON:0003075!4.75e-14!86;UBERON:0007284!4.75e-14!86;UBERON:0002346!8.94e-13!90;UBERON:0000956!1.27e-11!25;UBERON:0000203!1.27e-11!25;UBERON:0002619!1.94e-11!22;UBERON:0001950!1.77e-10!20;UBERON:0003056!4.97e-09!61;UBERON:0000468!4.11e-08!659;UBERON:0000062!2.89e-07!511
|ontology_enrichment_uberon=UBERON:0007023!3.37e-49!115;UBERON:0001049!8.62e-23!57;UBERON:0005068!8.62e-23!57;UBERON:0006241!8.62e-23!57;UBERON:0007135!8.62e-23!57;UBERON:0001017!2.88e-19!82;UBERON:0003080!1.11e-18!42;UBERON:0005743!4.27e-18!86;UBERON:0002780!4.58e-18!41;UBERON:0001890!4.58e-18!41;UBERON:0006240!4.58e-18!41;UBERON:0002616!1.93e-17!59;UBERON:0000073!1.12e-16!94;UBERON:0001016!1.12e-16!94;UBERON:0000955!2.12e-15!69;UBERON:0006238!2.12e-15!69;UBERON:0001893!2.25e-15!34;UBERON:0002020!3.81e-15!34;UBERON:0003528!3.81e-15!34;UBERON:0002791!7.53e-15!33;UBERON:0001869!1.43e-14!32;UBERON:0003075!4.75e-14!86;UBERON:0007284!4.75e-14!86;UBERON:0002346!8.94e-13!90;UBERON:0000956!1.27e-11!25;UBERON:0000203!1.27e-11!25;UBERON:0002619!1.94e-11!22;UBERON:0001950!1.77e-10!20;UBERON:0003056!4.97e-09!61;UBERON:0000468!4.11e-08!659;UBERON:0000062!2.89e-07!511
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190648587277783!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280542479871632!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321701993722114!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438029564835167!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666570282834431!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310087652789459!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140622456010284
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.00252127,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.000234347,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.0109386,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.0249033,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.0413643,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0538541,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.0695582,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.131316,0.198118,0.635872,0.563047,0.823736,9.12427e-06,0.0638737,0.0790073,0.261553,0.446302,0.373681,0.309233,0.0313047,0.330703,0.395854,0.061507,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.0643874,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.0407001,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.0280875,0.115044,0.373868,0.57762,0.608919,0.18237,0.126021,0.0020109,0.747852,0.275351,0.236471,0.185661,0.346319,0.179399,0.270984,0.258117,0.503058,0.513852,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.1002,0.305671,0.00134729,0.551561,0.448039,0.218623,0.0550136,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.0338328,0.294698,0.34331,0.000560159,0.289204,0.0605279,0.319027,0.278044,0.229008,0.108847,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.0150702,0.335105,0.144809,0.145539,0.08628,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.0142811,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.000539973,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.00358327,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,2.73054e-06,0.191777,0.111931,0.28934,0.0435386,0.0515253,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.0214786,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.0241568,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,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}}
}}

Revision as of 12:23, 5 September 2012


Full id: C4327_Mast_heart_spleen_aorta_penis_thyroid_CD34



Phase1 CAGE Peaks

Hg19::chr3:37493590..37493607,+p2@ITGA9
Hg19::chr3:37493612..37493651,+p1@ITGA9
Hg19::chr3:37493675..37493680,+p3@ITGA9


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.37e-49115
neural tube8.62e-2357
neural rod8.62e-2357
future spinal cord8.62e-2357
neural keel8.62e-2357
central nervous system2.88e-1982
anterior neural tube1.11e-1842
regional part of forebrain4.58e-1841
forebrain4.58e-1841
future forebrain4.58e-1841
regional part of brain1.93e-1759
regional part of nervous system1.12e-1694
nervous system1.12e-1694
brain2.12e-1569
future brain2.12e-1569
telencephalon2.25e-1534
gray matter3.81e-1534
brain grey matter3.81e-1534
regional part of telencephalon7.53e-1533
cerebral hemisphere1.43e-1432
neural plate4.75e-1486
presumptive neural plate4.75e-1486
neurectoderm8.94e-1390
cerebral cortex1.27e-1125
pallium1.27e-1125
regional part of cerebral cortex1.94e-1122
neocortex1.77e-1020
pre-chordal neural plate4.97e-0961
multi-cellular organism4.11e-08659
organ2.89e-07511


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#90536.336201576962630.003930750035764890.0190648587277783
CTCF#1066435.360256373075030.0064925092527670.0280542479871632
EGR1#195834.988179094810140.008056488137383440.0321701993722114
GATA2#2624312.7449317335540.0004829527704283790.00438029564835167
RAD21#5885310.35503389545630.0009004912073565420.00666570282834431
SMC3#9126315.04493284493280.0002935825420371870.00310087652789459
ZBTB7A#5134137.35190930787590.002516255860282270.0140622456010284



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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