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Coexpression cluster:C3264: Difference between revisions

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|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108991442973591
|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108991442973591
|tfbs_overrepresentation=2.36262e-05,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.0116452,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.00130254,0.132577,0.081977,0.0948982,0.0415721,0.00198832,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.00762432,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.00612307,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.00136001,0.0337251,0.227719,0.0952829,0.00708381,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,1.2603e-05,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.635872,0.563047,0.823736,0.807281,0.0638737,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.178727,0.248224,0.271958,0.292154,0.405773,0.39729,0.217139,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.0620388,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.155672,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.821217,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.258117,0.503058,0.513852,0.00691094,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.412837,0.671377,0.546839,0.551561,0.0225539,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.154921,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.858756,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.0460163,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.169823,0.284629,0.262537,0.010587,0.226257,0.405955,0.102469,0.363685,0.464871,0.753577,0.206222,0.525396,0.651524,0.020698,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.000203231,0.273024,0.262389,0.316179,0.0697683,0.0556835,0.00138994,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.00461664,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.00934729,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3264_migratory_melanoma_Dendritic_Melanocyte_mesenchymal_Saos2_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:19389788..19389791,+p12@PLEKHA5
Hg19::chr12:19389797..19389804,+p11@PLEKHA5
Hg19::chr12:19389814..19389872,+p2@PLEKHA5


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
conventional dendritic cell3.00e-108
melanocyte4.70e-0910
melanoblast4.70e-0910
dendritic cell3.28e-0810
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.42e-3553
regional part of brain2.42e-3553
neural tube2.93e-3556
neural rod2.93e-3556
future spinal cord2.93e-3556
neural keel2.93e-3556
regional part of forebrain2.45e-3341
forebrain2.45e-3341
anterior neural tube2.45e-3341
future forebrain2.45e-3341
telencephalon2.59e-2934
regional part of cerebral cortex6.91e-2922
cerebral hemisphere7.33e-2932
brain7.60e-2968
future brain7.60e-2968
central nervous system1.05e-2781
brain grey matter9.19e-2734
gray matter9.19e-2734
neural plate2.75e-2682
presumptive neural plate2.75e-2682
regional part of telencephalon4.63e-2632
neocortex5.43e-2520
cerebral cortex5.91e-2525
pallium5.91e-2525
neurectoderm1.32e-2486
nervous system5.77e-2489
pre-chordal neural plate6.24e-2261
ecto-epithelium1.22e-21104
adult organism1.08e-19114
structure with developmental contribution from neural crest5.42e-19132
ectoderm-derived structure1.08e-16171
ectoderm1.08e-16171
presumptive ectoderm1.08e-16171
gyrus5.62e-146
tube2.47e-10192
brainstem2.85e-096
anatomical conduit1.57e-08240
frontal cortex5.30e-083
parietal lobe8.94e-085
occipital lobe9.27e-085
medulla oblongata5.38e-073
myelencephalon5.38e-073
future myelencephalon5.38e-073
organ system subdivision8.78e-07223


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
ZNF263#1012738.221841637010680.001799043925565870.0108991442973591



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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