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Coexpression cluster:C3375: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129401709214999!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189530749300669!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278754850503488!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324194463323306!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321132609170491!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460829526695153!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246718692623042!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179692405911211!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127777547192989!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186093909870191!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029369939157484!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245833461366024!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0328972594773375
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129401709214999!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189530749300669!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278754850503488!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324194463323306!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321132609170491!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460829526695153!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246718692623042!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179692405911211!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127777547192989!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186093909870191!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029369939157484!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245833461366024!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0328972594773375
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.0347684,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.00444039,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.000830039,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.0133783,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0585224,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.00453939,0.063292,0.254773,0.446759,0.00386209,0.0380459,0.130174,0.584917,0.713218,0.451377,0.635872,0.563047,0.252249,0.0853552,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.217139,0.230901,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.0883629,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.236436,0.283727,0.314747,0.21363,0.291709,0.448095,0.576651,0.416816,0.292835,0.137839,0.439556,0.373868,0.57762,0.608919,0.18237,0.0359955,0.0964442,0.400457,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.412837,0.671377,0.188159,0.551561,0.448039,0.218623,0.0550136,0.695172,0.0451077,0.0747529,0.229003,0.28275,0.589326,0.0338328,0.294698,0.34331,0.138202,0.289204,0.327108,0.683186,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.0488795,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.00360191,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.166672,0.206222,0.525396,0.651524,0.113671,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.00427764,0.0627924,0.000143044,0.0179103,0.303939,0.0434097,0.0886747,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.016022,0.127758,0.175785,0.0181729,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.0443426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}}
}}

Revision as of 16:05, 26 November 2012


Full id: C3375_testis_parietal_brain_occipital_temporal_cerebellum_duodenum



Phase1 CAGE Peaks

Hg19::chr13:45915545..45915601,+p1@ENST00000412946
p1@ENST00000520590
p1@ENST00000520622
Hg19::chr15:77197781..77197801,-p3@SCAPER
Hg19::chr22:42486923..42487002,+p1@LOC100132273


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>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell1.36e-0752
lymphocyte2.37e-0753
common lymphoid progenitor2.37e-0753
nucleate cell6.72e-0755
Uber Anatomy
Ontology termp-valuen
adult organism1.13e-40114
neural tube7.41e-3156
neural rod7.41e-3156
future spinal cord7.41e-3156
neural keel7.41e-3156
regional part of nervous system3.98e-2953
regional part of brain3.98e-2953
nervous system2.46e-2789
central nervous system3.96e-2781
neurectoderm7.22e-2486
brain1.84e-2368
future brain1.84e-2368
regional part of forebrain2.79e-2341
forebrain2.79e-2341
anterior neural tube2.79e-2341
future forebrain2.79e-2341
neural plate1.02e-2282
presumptive neural plate1.02e-2282
telencephalon1.50e-1934
brain grey matter1.78e-1934
gray matter1.78e-1934
cerebral hemisphere9.57e-1932
regional part of telencephalon1.78e-1832
pre-chordal neural plate3.66e-1661
regional part of cerebral cortex7.34e-1622
ecto-epithelium1.29e-15104
cerebral cortex8.63e-1525
pallium8.63e-1525
neocortex1.03e-1420
ectoderm-derived structure6.17e-14171
ectoderm6.17e-14171
presumptive ectoderm6.17e-14171
structure with developmental contribution from neural crest5.28e-10132
posterior neural tube1.12e-0815
chordal neural plate1.12e-0815
organ system subdivision5.55e-08223
segmental subdivision of nervous system1.82e-0713
segmental subdivision of hindbrain4.51e-0712
hindbrain4.51e-0712
presumptive hindbrain4.51e-0712


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
ATF3#467322.46317452600878.81932387510763e-050.00129401709214999
CCNT2#90536.336201576962630.003930750035764890.0189530749300669
CTCF#1066435.360256373075030.0064925092527670.0278754850503488
E2F1#186934.907389214879320.008460985347239390.0324194463323306
E2F6#187635.017155731697390.00791769806886330.0321132609170491
ELF1#199734.258097958807540.01295179875054610.0460829526695153
HNF4A#3172215.42152690863580.005444210486686610.0246718692623042
HNF4G#3174219.16894835096450.003543986611284220.0179692405911211
IRF1#365937.63716375356390.002244692747297240.0127777547192989
MAX#414936.452555509007120.003721913834265510.0186093909870191
MYC#460935.22228187160940.007020843755740150.029369939157484
SP1#666735.69838137814090.005403962701712170.0245833461366024
TRIM28#10155212.39368336350830.008368344129438470.0328972594773375



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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