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Coexpression cluster:C1555: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0006947!3.47e-55!3;UBERON:0004054!3.47e-55!3;UBERON:0005904!1.27e-41!4;UBERON:0003135!4.99e-41!11;UBERON:0000473!8.30e-21!8;UBERON:0003101!1.20e-20!22;UBERON:0000079!1.20e-20!22;UBERON:0001301!8.95e-20!1;UBERON:0001000!1.30e-19!1;UBERON:0005352!1.30e-19!1;UBERON:0000998!1.56e-19!1;UBERON:0006868!1.56e-19!1;UBERON:0006834!3.91e-19!1;UBERON:0000489!1.03e-14!31;UBERON:0003133!2.02e-13!48;UBERON:0004175!5.38e-12!25;UBERON:0002113!1.39e-11!26;UBERON:0003918!1.39e-11!26;UBERON:0011143!1.39e-11!26;UBERON:0005095!1.39e-11!26;UBERON:0007687!1.39e-11!26;UBERON:0005156!6.78e-11!59;UBERON:0000990!6.78e-11!59;UBERON:0001255!3.58e-10!2;UBERON:0001556!3.58e-10!2;UBERON:0006554!9.81e-10!47;UBERON:0007023!1.23e-09!114;UBERON:0001008!1.56e-09!48;UBERON:0000058!2.58e-09!19;UBERON:0000080!4.09e-09!9;UBERON:0002120!4.09e-09!9;UBERON:0004875!4.09e-09!9;UBERON:0005721!4.09e-09!9;UBERON:0005754!4.09e-09!9;UBERON:0007297!4.09e-09!9;UBERON:0003886!2.05e-08!54;UBERON:0000991!2.51e-08!21;UBERON:0009196!2.51e-08!21;UBERON:0009117!2.51e-08!21;UBERON:0005564!2.51e-08!21;UBERON:0004176!5.66e-08!22;UBERON:0004876!1.28e-07!11;UBERON:0002553!1.89e-07!61;UBERON:0003887!4.71e-07!12;UBERON:0003103!9.88e-07!68
|ontology_enrichment_uberon=UBERON:0006947!3.47e-55!3;UBERON:0004054!3.47e-55!3;UBERON:0005904!1.27e-41!4;UBERON:0003135!4.99e-41!11;UBERON:0000473!8.30e-21!8;UBERON:0003101!1.20e-20!22;UBERON:0000079!1.20e-20!22;UBERON:0001301!8.95e-20!1;UBERON:0001000!1.30e-19!1;UBERON:0005352!1.30e-19!1;UBERON:0000998!1.56e-19!1;UBERON:0006868!1.56e-19!1;UBERON:0006834!3.91e-19!1;UBERON:0000489!1.03e-14!31;UBERON:0003133!2.02e-13!48;UBERON:0004175!5.38e-12!25;UBERON:0002113!1.39e-11!26;UBERON:0003918!1.39e-11!26;UBERON:0011143!1.39e-11!26;UBERON:0005095!1.39e-11!26;UBERON:0007687!1.39e-11!26;UBERON:0005156!6.78e-11!59;UBERON:0000990!6.78e-11!59;UBERON:0001255!3.58e-10!2;UBERON:0001556!3.58e-10!2;UBERON:0006554!9.81e-10!47;UBERON:0007023!1.23e-09!114;UBERON:0001008!1.56e-09!48;UBERON:0000058!2.58e-09!19;UBERON:0000080!4.09e-09!9;UBERON:0002120!4.09e-09!9;UBERON:0004875!4.09e-09!9;UBERON:0005721!4.09e-09!9;UBERON:0005754!4.09e-09!9;UBERON:0007297!4.09e-09!9;UBERON:0003886!2.05e-08!54;UBERON:0000991!2.51e-08!21;UBERON:0009196!2.51e-08!21;UBERON:0009117!2.51e-08!21;UBERON:0005564!2.51e-08!21;UBERON:0004176!5.66e-08!22;UBERON:0004876!1.28e-07!11;UBERON:0002553!1.89e-07!61;UBERON:0003887!4.71e-07!12;UBERON:0003103!9.88e-07!68
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.787587,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,1.54297,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,1.38854,0.417272,1.1597,0.413782,0.654459,1.00769,0.301779,1.06799,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.709554,0.240727,2.11876,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,1.96265,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
}}
}}

Revision as of 14:58, 26 November 2012


Full id: C1555_epididymis_kidney_seminal_ductus_uterus_colon_Cardiac



Phase1 CAGE Peaks

Hg19::chr10:102488914..102488920,+p@chr10:102488914..102488920
+
Hg19::chr18:72168431..72168467,+p@chr18:72168431..72168467
+
Hg19::chr2:177011059..177011079,+p@chr2:177011059..177011079
+
Hg19::chr2:177011092..177011100,+p@chr2:177011092..177011100
+
Hg19::chr6:111995736..111995753,-p@chr6:111995736..111995753
-


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
male genital duct3.47e-553
internal male genitalia3.47e-553
duct of male reproductive system1.27e-414
male reproductive organ4.99e-4111
testis8.30e-218
male organism1.20e-2022
male reproductive system1.20e-2022
epididymis8.95e-201
vas deferens1.30e-191
spermatic cord1.30e-191
seminal vesicle1.56e-191
seminal fluid secreting gland1.56e-191
uterus or analog3.91e-191
cavitated compound organ1.03e-1431
reproductive organ2.02e-1348
internal genitalia5.38e-1225
kidney1.39e-1126
kidney mesenchyme1.39e-1126
upper urinary tract1.39e-1126
kidney rudiment1.39e-1126
kidney field1.39e-1126
reproductive structure6.78e-1159
reproductive system6.78e-1159
urinary bladder3.58e-102
lower urinary tract3.58e-102
urinary system structure9.81e-1047
adult organism1.23e-09114
renal system1.56e-0948
duct2.58e-0919
mesonephros4.09e-099
pronephros4.09e-099
nephrogenic cord4.09e-099
pronephric mesoderm4.09e-099
rostral part of nephrogenic cord4.09e-099
presumptive pronephric mesoderm4.09e-099
body cavity precursor2.05e-0854
gonad2.51e-0821
indifferent external genitalia2.51e-0821
indifferent gonad2.51e-0821
gonad primordium2.51e-0821
external genitalia5.66e-0822
urogenital ridge1.28e-0711
anatomical cavity1.89e-0761
intraembryonic coelom4.71e-0712
compound organ9.88e-0768


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

No analysis results for this cluster

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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