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Coexpression cluster:C4061: Difference between revisions

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|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306826899050204!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.017451933333681!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457584946953605
|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306826899050204!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.017451933333681!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457584946953605
|tfbs_overrepresentation=0.000598099,0.0586687,0.134243,0.0477154,0.0214323,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,2.46009e-05,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.0236364,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.00762432,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.00252127,0.00446469,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.0148026,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,1.88972e-07,0.241734,0.062747,0.0857568,0.00125032,0.0953825,0.0473737,0.00375405,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.00442705,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.00087036,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.005305,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.00679439,0.0400322,0.127369,0.0403542,0.0547453,0.0172085,0.137725,0.00384591,0.0541353,0.0799324,0.00418474,0.140334,0.181817,0.0169639,0.0356339,0.158844,0.00782633,0.0274061,0.115574,0.0737247,0.118847,0.0178773,0.0401756,0.0828697,0.0160177,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,1.04552e-05,0.1129,0.312578,0.0151713,0.0142864,0.100942,4.37286e-05,0.10299,0.14193,0.37245,0.15606,0.0137227,0.0738599,0.126611,0.0101199,0.085973,0.060453,0.059896,0.0538541,0.384785,0.0418404,0.0765029,0.00475494,0.0931946,0.0472272,0.0381183,0.014161,0.0249262,0.182472,0.348993,0.00500828,0.0830921,0.116283,0.000475773,0.0815104,0.111647,0.0802194,0.00713165,0.159052,0.185164,0.01843,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.00453939,0.063292,0.254773,0.446759,0.00386209,0.000733101,0.130174,0.059488,0.0381789,0.451377,0.635872,0.051522,0.0319444,0.489965,0.0638737,0.261644,0.261553,0.118991,0.373681,0.309233,0.49143,0.0619618,0.0914012,0.329568,0.53472,0.0724671,0.00420832,0.292154,0.0964816,0.39729,0.581713,0.0643874,0.187251,0.0756284,0.181715,0.00249167,0.109988,0.0620388,0.0257868,0.107929,0.0821552,0.129235,0.280025,0.173877,0.168255,0.0117562,0.415647,0.142924,0.253571,0.0424424,0.0509673,0.141124,0.316882,0.0270783,0.155672,0.0669244,0.283727,0.000629694,0.0116619,0.0474194,0.448095,0.0563639,0.0175396,0.292835,0.137839,0.0210941,0.373868,0.213592,0.0694028,0.18237,0.346458,0.0964442,0.161148,0.275351,0.00267743,0.185661,0.0684159,0.179399,0.0405716,0.00341096,0.00573308,0.0367769,0.169228,0.0338468,0.00471332,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0138549,0.421596,0.581837,0.412837,0.671377,0.0462094,0.00142658,0.0225539,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.00241532,0.650179,0.061213,0.154921,0.0484563,0.0671437,0.0282052,0.289204,0.327108,0.319027,0.00452305,0.229008,0.108847,0.228096,0.336314,0.19763,0.0129079,0.20495,0.421464,0.48267,0.000256922,0.00092633,0.582303,0.335105,0.144809,0.0111455,0.0134194,0.0818086,0.447325,0.00044427,0.252232,0.152681,0.0465712,0.00985947,0.259235,0.134788,0.0985856,0.000172561,0.00541072,0.0450006,0.000938454,0.0526965,0.0524121,0.0144637,0.503082,0.522888,0.284629,1.69523e-05,0.359455,0.226257,0.0965765,0.00230458,0.0110128,0.464871,0.166672,0.206222,0.03988,0.0905337,0.00288466,0.040018,0.0654598,0.552319,0.281425,0.141758,0.0238793,0.0385377,0.159617,0.0310416,0.0119179,0.232251,0.00132186,0.0891382,0.0595618,0.524997,0.0178839,0.0688327,0.182325,0.34988,0.475069,0.0958562,0.273024,0.630264,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.0270501,0.0223093,0.442884,0.11631,0.0196924,0.111931,0.046606,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0842821,0.0179103,0.0517437,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.0200986,0.0684384,0.00127015,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,0.188694,0.0481795,0.0214786,0.406014,0.127758,0.175785,0.0181729,0.015204,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.1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}}
}}

Revision as of 16:31, 26 November 2012


Full id: C4061_throat_tongue_heart_skeletal_medial_left_occipital



Phase1 CAGE Peaks

Hg19::chr20:62127349..62127360,-p17@EEF1A2
Hg19::chr20:62127373..62127388,-p12@EEF1A2
Hg19::chr20:62129054..62129066,-p9@EEF1A2


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube8.18e-2256
neural rod8.18e-2256
future spinal cord8.18e-2256
neural keel8.18e-2256
regional part of nervous system8.51e-2253
regional part of brain8.51e-2253
adult organism1.64e-21114
central nervous system3.06e-2181
brain5.17e-2168
future brain5.17e-2168
regional part of cerebral cortex2.39e-1922
neocortex3.43e-1920
nervous system3.95e-1989
brain grey matter9.91e-1934
gray matter9.91e-1934
cerebral hemisphere1.40e-1832
regional part of forebrain7.46e-1841
forebrain7.46e-1841
anterior neural tube7.46e-1841
future forebrain7.46e-1841
telencephalon3.96e-1734
regional part of telencephalon9.03e-1732
cerebral cortex1.79e-1625
pallium1.79e-1625
neurectoderm7.80e-1686
neural plate5.02e-1582
presumptive neural plate5.02e-1582
ecto-epithelium4.09e-13104
pre-chordal neural plate9.42e-1161
structure with developmental contribution from neural crest1.24e-10132
ectoderm-derived structure1.64e-10171
ectoderm1.64e-10171
presumptive ectoderm1.64e-10171
gyrus7.81e-106
organ system subdivision1.62e-09223
Disease
Ontology termp-valuen
thoracic cancer2.25e-074
breast cancer2.25e-074
cell type cancer8.15e-07143


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
CTCFL#140690213.16431623931620.007433367036996010.0306826899050204
NANOG#79923219.49651898734180.003427255648501020.017451933333681
SMC3#9126210.02995522995520.0126656379767470.0457584946953605



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.