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Coexpression cluster:C363: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005631!5.48e-27!14;UBERON:0000158!5.48e-27!14;UBERON:0003124!9.45e-23!7;UBERON:0000478!1.02e-14!24;UBERON:0004119!9.43e-14!160;UBERON:0000925!9.43e-14!160;UBERON:0006595!9.43e-14!160;UBERON:0001987!2.14e-13!4;UBERON:0004340!2.14e-13!4;UBERON:0004923!4.99e-12!66;UBERON:0001949!1.38e-11!3;UBERON:0000476!4.27e-11!3;UBERON:0000920!4.27e-11!3;UBERON:0003100!5.75e-09!41;UBERON:0000161!7.13e-09!36;UBERON:0001708!9.31e-09!4;UBERON:0008895!9.31e-09!4;UBERON:0006554!1.01e-08!47;UBERON:0001911!1.20e-08!4;UBERON:0005333!1.20e-08!4;UBERON:0008425!1.20e-08!4;UBERON:0005311!1.20e-08!4;UBERON:0005153!1.59e-08!37;UBERON:0001008!1.76e-08!48;UBERON:0000305!5.39e-08!7;UBERON:0000077!1.89e-07!29;UBERON:0000344!2.41e-07!20;UBERON:0003350!4.48e-07!8;UBERON:0011159!4.54e-07!5;UBERON:0004871!5.42e-07!8;UBERON:0003102!9.48e-07!99
|ontology_enrichment_uberon=UBERON:0005631!5.48e-27!14;UBERON:0000158!5.48e-27!14;UBERON:0003124!9.45e-23!7;UBERON:0000478!1.02e-14!24;UBERON:0004119!9.43e-14!160;UBERON:0000925!9.43e-14!160;UBERON:0006595!9.43e-14!160;UBERON:0001987!2.14e-13!4;UBERON:0004340!2.14e-13!4;UBERON:0004923!4.99e-12!66;UBERON:0001949!1.38e-11!3;UBERON:0000476!4.27e-11!3;UBERON:0000920!4.27e-11!3;UBERON:0003100!5.75e-09!41;UBERON:0000161!7.13e-09!36;UBERON:0001708!9.31e-09!4;UBERON:0008895!9.31e-09!4;UBERON:0006554!1.01e-08!47;UBERON:0001911!1.20e-08!4;UBERON:0005333!1.20e-08!4;UBERON:0008425!1.20e-08!4;UBERON:0005311!1.20e-08!4;UBERON:0005153!1.59e-08!37;UBERON:0001008!1.76e-08!48;UBERON:0000305!5.39e-08!7;UBERON:0000077!1.89e-07!29;UBERON:0000344!2.41e-07!20;UBERON:0003350!4.48e-07!8;UBERON:0011159!4.54e-07!5;UBERON:0004871!5.42e-07!8;UBERON:0003102!9.48e-07!99
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|tfbs_overrepresentation_for_novel_motifs=0.392922,0.0231511,0.0433205,0.690252,0.126476,0.33591,0.143738,0.67282,0.42585,0.00186191,0.0880991,0.506588,0.0713726,0.137151,0.297708,0.340618,0.292499,0.401861,0.182982,0.252914,0.378549,0.41902,0.0988328,1.67052,0.0595477,0.183961,0.395825,0.663465,0.305717,0.199225,0.0782091,0.320373,0.160349,0.164228,0.0224141,0.00869988,0.0217109,0.103252,0.385811,0.096374,0.451618,0.0712053,0.351816,1.24464,0.00211418,0.439842,0.144369,0.0831196,0.603926,0.560353,0.193102,0.460977,0.211579,0.380845,1.26793,0.138819,0.572547,0.76841,0.33711,0.120144,0.352258,0.447153,0.950624,0.272031,0.156335,0.247273,0.586135,0.926911,0.312429,0.773993,0.0657842,0.698903,0.000687259,0.506934,0.459504,0.0174929,0.36042,0.259779,0.309955,0.208756,0.801766,0.271247,0.473085,0.255251,0.462965,4.78264e-05,0.0120958,0.0953162,0.210271,1.02207,0.670213,0.44026,1.59276,0.567475,0.0311054,0.370668,0.767059,0.366883,0.213366,0.0749883,0.200679,0.328967,0.362441,0.801007,0.239166,0.0860038,0.283454,0.420506,0.0594507,0.272108,0.708091,0.360242,0.657388,0.308638,0.626724,0.719246,0.00774327,0.565681,0.245619,0.174534,1.24902,0.600521,0.680027,0.162926,0.727676,0.721301,0.853167,0.337232,0.536756,0.0738886,0.440837,0.0794722,2.32322,0.484932,0.681963,0.172412,1.40984,0.0980487,0.643378,1.46638,1.07263,0.609773,0.141077,0.364073,0.675164,0.371522,0.228804,1.30966,0.0698156,0.0130645,0.436549,0.000823141,0.441156,0.227123,0.145462,0.802573,0.199535,1.18721,0.0595702,0.18416,0.608684,0.425737,1.50733,0.735745,2.00379,0.471911,0.301615,0.440174,0.000749849
}}
}}

Revision as of 14:09, 26 November 2012


Full id: C363_Mallassezderived_Gingival_Keratinocyte_Mammary_Prostate_Small_Urothelial



Phase1 CAGE Peaks

Hg19::chr18:21452899..21452910,+p2@LAMA3
Hg19::chr18:21452964..21452993,+p1@LAMA3
Hg19::chr18:21461943..21461955,+p@chr18:21461943..21461955
+
Hg19::chr18:21464760..21464772,+p2@X77598
Hg19::chr18:21474288..21474320,-p@chr18:21474288..21474320
-
Hg19::chr18:21474914..21474939,+p@chr18:21474914..21474939
+
Hg19::chr18:21474947..21474966,+p@chr18:21474947..21474966
+
Hg19::chr18:21478695..21478707,+p9@LAMA3
Hg19::chr18:21478968..21478985,-p@chr18:21478968..21478985
-
Hg19::chr18:21478996..21479008,-p@chr18:21478996..21479008
-
Hg19::chr18:21479321..21479334,+p@chr18:21479321..21479334
+
Hg19::chr18:21479368..21479399,-p@chr18:21479368..21479399
-
Hg19::chr18:21479408..21479415,-p@chr18:21479408..21479415
-
Hg19::chr18:21481109..21481120,+p@chr18:21481109..21481120
+
Hg19::chr18:21481125..21481150,+p@chr18:21481125..21481150
+
Hg19::chr18:21481209..21481225,+p@chr18:21481209..21481225
+
Hg19::chr18:21483933..21483967,-p@chr18:21483933..21483967
-
Hg19::chr18:21483996..21484010,+p@chr18:21483996..21484010
+
Hg19::chr18:21484533..21484572,+p@chr18:21484533..21484572
+
Hg19::chr18:21484604..21484624,+p@chr18:21484604..21484624
+
Hg19::chr18:21485515..21485536,-p@chr18:21485515..21485536
-
Hg19::chr18:21485558..21485596,-p@chr18:21485558..21485596
-
Hg19::chr18:21487576..21487588,-p@chr18:21487576..21487588
-
Hg19::chr18:21487788..21487807,+p@chr18:21487788..21487807
+
Hg19::chr18:21487848..21487862,-p@chr18:21487848..21487862
-
Hg19::chr18:21494675..21494689,+p@chr18:21494675..21494689
+
Hg19::chr18:21500893..21500904,+p@chr18:21500893..21500904
+
Hg19::chr18:21508639..21508652,+p@chr18:21508639..21508652
+
Hg19::chr18:21529811..21529823,+p@chr18:21529811..21529823
+
Hg19::chr18:21531667..21531694,+p@chr18:21531667..21531694
+
Hg19::chr3:129513704..129513729,-p12@TMCC1


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

GO IDGO nameFDR corrected p-value
GO:0045995regulation of embryonic development0.00988889675790024
GO:0005606laminin-1 complex0.00988889675790024
GO:0043256laminin complex0.00988889675790024
GO:0005605basal lamina0.0182777618173525
GO:0030334regulation of cell migration0.0182777618173525
GO:0030155regulation of cell adhesion0.0182777618173525
GO:0051270regulation of cell motility0.0182777618173525
GO:0040012regulation of locomotion0.0182777618173525
GO:0040011locomotion0.0182777618173525
GO:0005604basement membrane0.0182777618173525
GO:0044420extracellular matrix part0.0277102104427011
GO:0008544epidermis development0.0277102104427011
GO:0007398ectoderm development0.0277102104427011
GO:0016477cell migration0.0363450637728375
GO:0009790embryonic development0.0363450637728375
GO:0050793regulation of developmental process0.0363450637728375
GO:0009888tissue development0.0441633001453489
GO:0051674localization of cell0.0495626658089424
GO:0006928cell motility0.0495626658089424



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
extraembryonic membrane5.48e-2714
membranous layer5.48e-2714
chorion9.45e-237
extraembryonic structure1.02e-1424
endoderm-derived structure9.43e-14160
endoderm9.43e-14160
presumptive endoderm9.43e-14160
placenta2.14e-134
allantois2.14e-134
organ component layer4.99e-1266
gingival epithelium1.38e-113
acellular anatomical structure4.27e-113
egg chorion4.27e-113
female organism5.75e-0941
orifice7.13e-0936
jaw skeleton9.31e-094
splanchnocranium9.31e-094
urinary system structure1.01e-0847
mammary gland1.20e-084
mammary bud1.20e-084
mammary ridge1.20e-084
mammary placode1.20e-084
epithelial bud1.59e-0837
renal system1.76e-0848
amnion5.39e-087
mixed endoderm/mesoderm-derived structure1.89e-0729
mucosa2.41e-0720
epithelium of mucosa4.48e-078
primary subdivision of cranial skeletal system4.54e-075
somatic layer of lateral plate mesoderm5.42e-078
surface structure9.48e-0799
Disease
Ontology termp-valuen
squamous cell carcinoma4.05e-1014


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)

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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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