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Coexpression cluster:C4005: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00109972600218089!BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778099213425116!BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000527412054872534!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279801590265632!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915828131347991!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136792412966105!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186773476329452!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195083507946979!MEF2C#4208;3:41.3113544926241:1.41744912101957e-05:0.000340471409269004!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269857930738612!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173087048443791!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883106568062126!REST#5978;3:9.65002871612802:0.00111263624711459:0.007685866592526!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024684414826982!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109171838871223!SRF#6722;3:13.7971782621678:0.000380661502580019:0.003754453363675!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629810047883878
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00109972600218089!BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778099213425116!BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000527412054872534!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279801590265632!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915828131347991!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136792412966105!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186773476329452!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195083507946979!MEF2C#4208;3:41.3113544926241:1.41744912101957e-05:0.000340471409269004!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269857930738612!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173087048443791!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883106568062126!REST#5978;3:9.65002871612802:0.00111263624711459:0.007685866592526!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024684414826982!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109171838871223!SRF#6722;3:13.7971782621678:0.000380661502580019:0.003754453363675!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629810047883878
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.00295997,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.000126043,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.0015841,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.00234165,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.000171422,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,9.48809e-05,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.0356268,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.355018,0.782949,0.268011,0.20128,0.823736,0.807281,0.335423,0.261644,0.261553,0.446302,0.0806291,0.053682,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.39729,0.0582602,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.107929,0.0821552,0.463191,0.0883629,0.173877,0.520763,0.370782,0.415647,0.484505,0.00335333,0.276829,0.0509673,0.481778,0.316882,0.223503,0.503224,0.236436,0.00483199,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.0280875,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.821217,0.747852,0.275351,0.236471,0.0012387,0.346319,0.535598,0.270984,0.0772647,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.581837,0.412837,0.671377,0.546839,0.191921,0.448039,0.218623,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.28275,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.858756,0.335105,0.144809,0.145539,0.08628,0.376191,0.447325,0.127215,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.00696513,0.284629,0.262537,0.359455,0.226257,0.0965765,0.41707,0.363685,0.00388249,0.753577,0.206222,0.03988,0.651524,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.00132186,0.0891382,0.0595618,0.00710886,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,5.97226e-05,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.116981,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.000250525,0.00210526,0.00817962,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.2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}}
}}

Revision as of 16:29, 26 November 2012


Full id: C4005_small_colon_acute_Burkitt_Intestinal_renal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:9129598..9129610,-p3@SLC2A5
Hg19::chr1:9129614..9129619,-p6@SLC2A5
Hg19::chr1:9129631..9129664,-p2@SLC2A5


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 organism1.23e-27114
neural tube1.44e-2756
neural rod1.44e-2756
future spinal cord1.44e-2756
neural keel1.44e-2756
regional part of nervous system1.30e-2653
regional part of brain1.30e-2653
regional part of forebrain1.04e-2041
forebrain1.04e-2041
anterior neural tube1.04e-2041
future forebrain1.04e-2041
telencephalon1.45e-1934
brain grey matter1.77e-1934
gray matter1.77e-1934
brain2.63e-1968
future brain2.63e-1968
regional part of telencephalon8.49e-1832
central nervous system8.68e-1881
cerebral hemisphere1.14e-1732
nervous system7.20e-1689
neural plate2.17e-1582
presumptive neural plate2.17e-1582
neurectoderm1.18e-1486
regional part of cerebral cortex5.53e-1322
cerebral cortex7.30e-1225
pallium7.30e-1225
pre-chordal neural plate9.00e-1261
ecto-epithelium1.56e-11104
neocortex2.85e-1120
neural nucleus8.60e-109
nucleus of brain8.60e-109
structure with developmental contribution from neural crest1.93e-08132
telencephalic nucleus4.74e-087
posterior neural tube5.13e-0815
chordal neural plate5.13e-0815
basal ganglion1.00e-079
nuclear complex of neuraxis1.00e-079
aggregate regional part of brain1.00e-079
collection of basal ganglia1.00e-079
cerebral subcortex1.00e-079
segmental subdivision of hindbrain3.80e-0712
hindbrain3.80e-0712
presumptive hindbrain3.80e-0712
brainstem4.62e-076


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
BATF#10538324.35780179230366.91705216281876e-050.00109972600218089
BCL11A#53335328.36945510360714.37778126761649e-050.000778099213425116
BCL3#602334.54710280373832.42397750207122e-050.000527412054872534
CTCF#1066435.360256373075030.0064925092527670.0279801590265632
EBF1#187938.9064668465690.00141523283560980.00915828131347991
IRF4#3662321.91451268674419.49854535978121e-050.00136792412966105
MAX#414936.452555509007120.003721913834265510.0186773476329452
MEF2A#4205318.74323090964410.0001518243905622470.00195083507946979
MEF2C#4208341.31135449262411.41744912101957e-050.000340471409269004
NFKB1#479035.488063424193840.006049381815655430.0269857930738612
PAX5#507936.669565531177830.003370290999677260.0173087048443791
POU2F2#545239.106124057742520.001324165192682130.00883106568062126
REST#597839.650028716128020.001112636247114590.007685866592526
SP1#666735.69838137814090.005403962701712170.024684414826982
SPI1#668838.204323508522730.001810593189410520.0109171838871223
SRF#6722313.79717826216780.0003806615025800190.003754453363675
TCF12#6938310.63446490218640.0008313523990202070.00629810047883878



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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