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Coexpression cluster:C4273: Difference between revisions

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|tf_chipseq_enrich=YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330354537581262
|tf_chipseq_enrich=YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330354537581262
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.00156205,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.000504333,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.0175714,0.111283,0.121201,0.154071,0.0541794,0.00252127,0.0929951,0.00153794,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.0117644,0.108602,0.0759481,0.054569,0.0504887,0.00989266,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.0472875,0.0347684,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.0124568,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.000695613,0.0259741,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.0101452,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.000155255,0.116642,0.147788,0.273479,0.114283,0.0400322,0.00847953,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.0176328,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.00127354,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0042906,0.15185,0.0229156,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.059488,0.713218,0.198118,0.635872,0.051522,0.0986134,0.807281,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.0313047,0.0619618,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.000290219,0.597171,0.187251,0.362792,2.28809e-06,0.423979,0.109988,0.330894,0.218329,0.427027,0.0821552,0.00381454,0.0883629,0.00734087,0.03861,0.0792797,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.0565541,0.223503,0.503224,0.0669244,0.283727,0.314747,0.0116619,0.291709,3.68979e-05,0.576651,0.0175396,0.0478086,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.821217,0.0512465,0.275351,0.236471,0.185661,0.346319,0.0427964,0.00415948,0.00341096,0.503058,0.513852,0.169228,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.00204647,0.412837,0.00570056,0.546839,0.551561,0.120021,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.0284893,0.0897888,0.00223439,0.50215,0.294698,0.34331,0.138202,0.289204,0.0077225,0.319027,0.278044,0.807485,0.428671,0.228096,0.0642385,0.19763,0.15631,0.0530502,0.421464,0.141711,0.420626,0.165111,0.858756,0.0637439,0.144809,0.145539,0.08628,0.376191,0.447325,0.127215,0.252232,0.0122989,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.155572,0.522888,0.284629,0.00375279,0.010587,0.226257,0.405955,0.41707,0.00121543,0.464871,0.40841,0.206222,0.00103554,0.0224921,0.437176,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.182325,0.0699395,0.136757,0.00199596,0.273024,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.00643465,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897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}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4273_ductus_epididymis_seminal_parotid_hippocampus_retina_submaxillary



Phase1 CAGE Peaks

Hg19::chr3:121613224..121613254,+p2@SLC15A2
Hg19::chr3:121613265..121613295,+p1@SLC15A2
Hg19::chr3:121613301..121613313,+p3@SLC15A2


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 organism9.94e-74114
neural tube1.60e-5656
neural rod1.60e-5656
future spinal cord1.60e-5656
neural keel1.60e-5656
regional part of nervous system4.23e-5353
regional part of brain4.23e-5353
central nervous system4.31e-5081
regional part of forebrain4.21e-4741
forebrain4.21e-4741
anterior neural tube4.21e-4741
future forebrain4.21e-4741
neurectoderm4.57e-4686
neural plate2.37e-4582
presumptive neural plate2.37e-4582
nervous system9.71e-4589
telencephalon2.80e-4234
brain grey matter8.29e-4234
gray matter8.29e-4234
brain8.28e-4168
future brain8.28e-4168
cerebral hemisphere4.24e-4032
regional part of telencephalon1.19e-3932
pre-chordal neural plate1.03e-3661
ecto-epithelium4.06e-34104
cerebral cortex3.45e-3125
pallium3.45e-3125
structure with developmental contribution from neural crest2.26e-30132
ectoderm-derived structure3.62e-30171
ectoderm3.62e-30171
presumptive ectoderm3.62e-30171
organ system subdivision5.82e-30223
regional part of cerebral cortex5.36e-2922
neocortex3.82e-2620
anatomical cluster2.18e-16373
multi-tissue structure3.05e-13342
anatomical conduit6.41e-13240
basal ganglion1.64e-129
nuclear complex of neuraxis1.64e-129
aggregate regional part of brain1.64e-129
collection of basal ganglia1.64e-129
cerebral subcortex1.64e-129
neural nucleus6.60e-129
nucleus of brain6.60e-129
embryo3.33e-11592
tube4.02e-11192
posterior neural tube8.79e-1115
chordal neural plate8.79e-1115
organ part2.44e-10218
organ4.50e-10503
temporal lobe7.46e-106
telencephalic nucleus7.56e-107
embryonic structure1.62e-09564
multi-cellular organism2.76e-09656
developing anatomical structure3.31e-09581
germ layer5.92e-09560
germ layer / neural crest5.92e-09560
embryonic tissue5.92e-09560
presumptive structure5.92e-09560
germ layer / neural crest derived structure5.92e-09560
epiblast (generic)5.92e-09560
segmental subdivision of nervous system9.67e-0913
gyrus1.25e-086
brainstem1.68e-086
limbic system1.80e-085
segmental subdivision of hindbrain7.95e-0812
hindbrain7.95e-0812
presumptive hindbrain7.95e-0812
epithelium1.82e-07306
parietal lobe2.32e-075
cell layer3.25e-07309
occipital lobe3.91e-075
corpus striatum4.78e-074
striatum4.78e-074
ventral part of telencephalon4.78e-074
future corpus striatum4.78e-074


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
YY1#752834.911170749853860.008441455341808260.0330354537581262



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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