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Coexpression cluster:C835: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.51e-36!114;UBERON:0001049!2.22e-35!56;UBERON:0005068!2.22e-35!56;UBERON:0006241!2.22e-35!56;UBERON:0007135!2.22e-35!56;UBERON:0000073!2.95e-29!53;UBERON:0002616!2.95e-29!53;UBERON:0001017!6.60e-24!81;UBERON:0003075!5.66e-22!82;UBERON:0007284!5.66e-22!82;UBERON:0000955!4.60e-21!68;UBERON:0006238!4.60e-21!68;UBERON:0001016!7.91e-21!89;UBERON:0002346!1.25e-20!86;UBERON:0002298!6.06e-20!6;UBERON:0003076!6.53e-20!15;UBERON:0003057!6.53e-20!15;UBERON:0002780!9.14e-19!41;UBERON:0001890!9.14e-19!41;UBERON:0003080!9.14e-19!41;UBERON:0006240!9.14e-19!41;UBERON:0003528!1.58e-18!34;UBERON:0002020!1.58e-18!34;UBERON:0001893!5.17e-18!34;UBERON:0010371!7.28e-16!104;UBERON:0002791!1.13e-14!32;UBERON:0010314!1.36e-14!132;UBERON:0001869!1.61e-14!32;UBERON:0000489!1.89e-14!31;UBERON:0004733!1.33e-12!12;UBERON:0002028!1.33e-12!12;UBERON:0007277!1.33e-12!12;UBERON:0000125!2.34e-12!9;UBERON:0002308!2.34e-12!9;UBERON:0000025!1.17e-11!192;UBERON:0004111!1.43e-11!240;UBERON:0004732!1.51e-11!13;UBERON:0003056!2.61e-11!61;UBERON:0006947!2.70e-11!3;UBERON:0004054!2.70e-11!3;UBERON:0002619!4.57e-11!22;UBERON:0000988!6.60e-11!3;UBERON:0001896!9.15e-11!3;UBERON:0005290!9.15e-11!3;UBERON:0010096!9.15e-11!3;UBERON:0000476!1.75e-10!3;UBERON:0000920!1.75e-10!3;UBERON:0002240!2.82e-10!3;UBERON:0005174!2.82e-10!3;UBERON:0001137!2.82e-10!3;UBERON:0001950!6.78e-10!20;UBERON:0000956!1.44e-09!25;UBERON:0000203!1.44e-09!25;UBERON:0011216!2.01e-09!223;UBERON:0000477!3.23e-09!373;UBERON:0005904!1.48e-08!4;UBERON:0004121!1.67e-08!171;UBERON:0000924!1.67e-08!171;UBERON:0006601!1.67e-08!171;UBERON:0002113!1.90e-08!26;UBERON:0003918!1.90e-08!26;UBERON:0011143!1.90e-08!26;UBERON:0005095!1.90e-08!26;UBERON:0007687!1.90e-08!26;UBERON:0002420!2.47e-08!9;UBERON:0007245!2.47e-08!9;UBERON:0010009!2.47e-08!9;UBERON:0010011!2.47e-08!9;UBERON:0000454!2.47e-08!9;UBERON:0000481!2.64e-08!342;UBERON:0000062!2.92e-08!503;UBERON:0002148!7.11e-08!2;UBERON:0006331!7.11e-08!2;UBERON:0009662!7.11e-08!2;UBERON:0003124!1.42e-07!7;UBERON:0000341!1.56e-07!2;UBERON:0009663!2.73e-07!7;UBERON:0000064!3.64e-07!218;UBERON:0003127!3.70e-07!2;UBERON:0006554!4.08e-07!47;UBERON:0003103!5.63e-07!68;UBERON:0001008!6.46e-07!48
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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.101185,0.273994,0.404877,0.237701,0.403356,0.474413,0.140612,0.429396,0.0921938,0.375531,0.515448,0.107365,0.46359,0.666154,0.256724,0.68716,0.191625,0.116269,0.178097,0.274046,0.0265279,0.396189,0.233338,0.314616,0.537051,0.310025,0.39419,0.240354,0.0826403,0.355553,0.722879,0.165252,0.108961,0.20845,0.359459,0.20579,0.404426,1.04488,0.789486,0.207288,0.340749,0.031261,0.235234,0.111933,0.301189,0.47544,0.365597,0.518466,0.240465,0.550604,0.486559,0.214602,0.797754,0.947672,0.466348,0.244111,0.435652,0.281305,0.434711,0.762758,0.477672,0.430344,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.210881,0.945703,0.104203,0.316793,0.0867529,0.644006,0.709631,0.309107,0.11972,0.659298,1.23725,0.142768,0.89511,0.140048,1.08278,0.575051,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.670367,0.53563,0.368981,0.780743,0.579925,0.0696508,1.04928,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.7752,0.772599,0.269151,0.384185,1.07963,1.11599,0.0648813,0.354459,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.537508,0.869279,0.358161,0.993705,0.50181,1.13991,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,1.49832,0.42776,0.601672,1.79367,0.337738,0.168379,0.429078,0.0287097,0.869654,0.132719,1.2007,1.26919,0.560015,0.225815,0.314669,0.786832,1.05976,0.851493,0.708865,0.291837,0.633206,1.23566,0.158769,0.473159,0.140569
}}
}}

Revision as of 14:30, 26 November 2012


Full id: C835_kidney_thyroid_mesothelioma_throat_salivary_seminal_chorionic



Phase1 CAGE Peaks

Hg19::chr15:54051846..54051904,-p1@WDR72
Hg19::chr16:66731112..66731127,-p@chr16:66731112..66731127
-
Hg19::chr17:68071389..68071396,+p7@KCNJ16
Hg19::chr17:68128382..68128407,+p10@KCNJ16
Hg19::chr17:68130458..68130470,+p@chr17:68130458..68130470
+
Hg19::chr17:68130693..68130703,+p@chr17:68130693..68130703
+
Hg19::chr17:68130841..68130856,+p@chr17:68130841..68130856
+
Hg19::chr17:68131022..68131042,+p@chr17:68131022..68131042
+
Hg19::chr17:68131163..68131167,+p@chr17:68131163..68131167
+
Hg19::chr9:132962655..132962688,+p9@NCS1


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:0005242inward rectifier potassium channel activity0.0275521017308371
GO:0030955potassium ion binding0.0380313199105145
GO:0005249voltage-gated potassium channel activity0.0380313199105145
GO:0005267potassium channel activity0.0380313199105145
GO:0031420alkali metal ion binding0.0380313199105145
GO:0022843voltage-gated cation channel activity0.0380313199105145
GO:0006813potassium ion transport0.0380313199105145
GO:0005244voltage-gated ion channel activity0.0380313199105145
GO:0022832voltage-gated channel activity0.0380313199105145
GO:0005261cation channel activity0.0410926645472742
GO:0046873metal ion transmembrane transporter activity0.0410926645472742
GO:0022836gated channel activity0.0410926645472742
GO:0015672monovalent inorganic cation transport0.0410926645472742
GO:0005216ion channel activity0.0410926645472742
GO:0030001metal ion transport0.0410926645472742
GO:0022838substrate specific channel activity0.0410926645472742
GO:0015267channel activity0.0410926645472742
GO:0022803passive transmembrane transporter activity0.0410926645472742
GO:0006812cation transport0.0461497703991522
GO:0008324cation transmembrane transporter activity0.0461497703991522



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>

Cell Type
Ontology termp-valuen
chorionic membrane mesenchymal stem cell1.75e-103
Uber Anatomy
Ontology termp-valuen
adult organism2.51e-36114
neural tube2.22e-3556
neural rod2.22e-3556
future spinal cord2.22e-3556
neural keel2.22e-3556
regional part of nervous system2.95e-2953
regional part of brain2.95e-2953
central nervous system6.60e-2481
neural plate5.66e-2282
presumptive neural plate5.66e-2282
brain4.60e-2168
future brain4.60e-2168
nervous system7.91e-2189
neurectoderm1.25e-2086
brainstem6.06e-206
posterior neural tube6.53e-2015
chordal neural plate6.53e-2015
regional part of forebrain9.14e-1941
forebrain9.14e-1941
anterior neural tube9.14e-1941
future forebrain9.14e-1941
brain grey matter1.58e-1834
gray matter1.58e-1834
telencephalon5.17e-1834
ecto-epithelium7.28e-16104
regional part of telencephalon1.13e-1432
structure with developmental contribution from neural crest1.36e-14132
cerebral hemisphere1.61e-1432
cavitated compound organ1.89e-1431
segmental subdivision of hindbrain1.33e-1212
hindbrain1.33e-1212
presumptive hindbrain1.33e-1212
neural nucleus2.34e-129
nucleus of brain2.34e-129
tube1.17e-11192
anatomical conduit1.43e-11240
segmental subdivision of nervous system1.51e-1113
pre-chordal neural plate2.61e-1161
male genital duct2.70e-113
internal male genitalia2.70e-113
regional part of cerebral cortex4.57e-1122
pons6.60e-113
medulla oblongata9.15e-113
myelencephalon9.15e-113
future myelencephalon9.15e-113
acellular anatomical structure1.75e-103
egg chorion1.75e-103
spinal cord2.82e-103
dorsal region element2.82e-103
dorsum2.82e-103
neocortex6.78e-1020
cerebral cortex1.44e-0925
pallium1.44e-0925
organ system subdivision2.01e-09223
anatomical cluster3.23e-09373
duct of male reproductive system1.48e-084
ectoderm-derived structure1.67e-08171
ectoderm1.67e-08171
presumptive ectoderm1.67e-08171
kidney1.90e-0826
kidney mesenchyme1.90e-0826
upper urinary tract1.90e-0826
kidney rudiment1.90e-0826
kidney field1.90e-0826
basal ganglion2.47e-089
nuclear complex of neuraxis2.47e-089
aggregate regional part of brain2.47e-089
collection of basal ganglia2.47e-089
cerebral subcortex2.47e-089
multi-tissue structure2.64e-08342
organ2.92e-08503
locus ceruleus7.11e-082
brainstem nucleus7.11e-082
hindbrain nucleus7.11e-082
chorion1.42e-077
throat1.56e-072
telencephalic nucleus2.73e-077
organ part3.64e-07218
open tracheal system trachea3.70e-072
urinary system structure4.08e-0747
compound organ5.63e-0768
renal system6.46e-0748
Disease
Ontology termp-valuen
clear cell adenocarcinoma7.53e-072


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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