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Coexpression cluster:C835: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!9.98e-42!115;UBERON:0001049!2.84e-37!57;UBERON:0005068!2.84e-37!57;UBERON:0006241!2.84e-37!57;UBERON:0007135!2.84e-37!57;UBERON:0001017!1.63e-31!82;UBERON:0005743!2.96e-31!86;UBERON:0002616!4.35e-31!59;UBERON:0003075!9.30e-31!86;UBERON:0007284!9.30e-31!86;UBERON:0002346!4.28e-29!90;UBERON:0000955!1.31e-27!69;UBERON:0006238!1.31e-27!69;UBERON:0000073!6.65e-26!94;UBERON:0001016!6.65e-26!94;UBERON:0003080!1.56e-24!42;UBERON:0002780!4.49e-24!41;UBERON:0001890!4.49e-24!41;UBERON:0006240!4.49e-24!41;UBERON:0000153!2.08e-20!129;UBERON:0007811!2.08e-20!129;UBERON:0002020!7.78e-20!34;UBERON:0003528!7.78e-20!34;UBERON:0001893!2.23e-19!34;UBERON:0000033!4.07e-19!123;UBERON:0003056!4.21e-19!61;UBERON:0002791!1.06e-18!33;UBERON:0001869!6.82e-18!32;UBERON:0004121!7.65e-16!169;UBERON:0000924!2.59e-15!173;UBERON:0006601!2.59e-15!173;UBERON:0000062!1.15e-14!511;UBERON:0002619!1.98e-14!22;UBERON:0003076!5.07e-14!15;UBERON:0003057!5.07e-14!15;UBERON:0000064!3.72e-13!219;UBERON:0000956!5.73e-13!25;UBERON:0000203!5.73e-13!25;UBERON:0001950!7.60e-13!20;UBERON:0000481!4.11e-12!347;UBERON:0000477!8.56e-12!286;UBERON:0004733!1.95e-11!12;UBERON:0002028!1.95e-11!12;UBERON:0007277!1.95e-11!12;UBERON:0004111!3.68e-11!241;UBERON:0000025!5.11e-11!194;UBERON:0000922!1.82e-10!612;UBERON:0004732!3.36e-10!13;UBERON:0000489!3.10e-09!32;UBERON:0000468!3.17e-09!659;UBERON:0002308!1.12e-08!9;UBERON:0000125!1.12e-08!9;UBERON:0002680!1.21e-08!9;UBERON:0001895!1.21e-08!9;UBERON:0010092!1.21e-08!9;UBERON:0000475!1.76e-08!365;UBERON:0002298!1.86e-08!8;UBERON:0002420!2.42e-08!9;UBERON:0007245!2.42e-08!9;UBERON:0010009!2.42e-08!9;UBERON:0010011!2.42e-08!9;UBERON:0000454!2.42e-08!9;UBERON:0002050!2.63e-08!605;UBERON:0005423!2.63e-08!605;UBERON:0000467!4.26e-08!625;UBERON:0000923!5.22e-08!604;UBERON:0005291!5.22e-08!604;UBERON:0006598!5.22e-08!604;UBERON:0002532!5.22e-08!604;UBERON:0000480!5.35e-08!626;UBERON:0000483!1.13e-07!309;UBERON:0000119!2.46e-07!312;UBERON:0002113!2.66e-07!27;UBERON:0003918!2.66e-07!27;UBERON:0005095!2.66e-07!27;UBERON:0007687!2.66e-07!27;UBERON:0001871!8.14e-07!7;UBERON:0009663!8.65e-07!7
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}}
}}

Revision as of 20:53, 8 August 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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism9.98e-42115
neural tube2.84e-3757
neural rod2.84e-3757
future spinal cord2.84e-3757
neural keel2.84e-3757
central nervous system1.63e-3182
regional part of brain4.35e-3159
neural plate9.30e-3186
presumptive neural plate9.30e-3186
neurectoderm4.28e-2990
brain1.31e-2769
future brain1.31e-2769
regional part of nervous system6.65e-2694
nervous system6.65e-2694
anterior neural tube1.56e-2442
regional part of forebrain4.49e-2441
forebrain4.49e-2441
future forebrain4.49e-2441
anterior region of body2.08e-20129
craniocervical region2.08e-20129
gray matter7.78e-2034
brain grey matter7.78e-2034
telencephalon2.23e-1934
head4.07e-19123
pre-chordal neural plate4.21e-1961
regional part of telencephalon1.06e-1833
cerebral hemisphere6.82e-1832
ectoderm-derived structure7.65e-16169
ectoderm2.59e-15173
presumptive ectoderm2.59e-15173
organ1.15e-14511
regional part of cerebral cortex1.98e-1422
posterior neural tube5.07e-1415
chordal neural plate5.07e-1415
organ part3.72e-13219
cerebral cortex5.73e-1325
pallium5.73e-1325
neocortex7.60e-1320
multi-tissue structure4.11e-12347
anatomical cluster8.56e-12286
segmental subdivision of hindbrain1.95e-1112
hindbrain1.95e-1112
presumptive hindbrain1.95e-1112
anatomical conduit3.68e-11241
tube5.11e-11194
embryo1.82e-10612
segmental subdivision of nervous system3.36e-1013
cavitated compound organ3.10e-0932
multi-cellular organism3.17e-09659
nucleus of brain1.12e-089
neural nucleus1.12e-089
regional part of metencephalon1.21e-089
metencephalon1.21e-089
future metencephalon1.21e-089
organism subdivision1.76e-08365
brainstem1.86e-088
basal ganglion2.42e-089
nuclear complex of neuraxis2.42e-089
aggregate regional part of brain2.42e-089
collection of basal ganglia2.42e-089
cerebral subcortex2.42e-089
embryonic structure2.63e-08605
developing anatomical structure2.63e-08605
anatomical system4.26e-08625
germ layer5.22e-08604
embryonic tissue5.22e-08604
presumptive structure5.22e-08604
epiblast (generic)5.22e-08604
anatomical group5.35e-08626
epithelium1.13e-07309
cell layer2.46e-07312
kidney2.66e-0727
kidney mesenchyme2.66e-0727
kidney rudiment2.66e-0727
kidney field2.66e-0727
temporal lobe8.14e-077
telencephalic nucleus8.65e-077


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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