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Coexpression cluster:C449: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:23, 17 September 2013


Full id: C449_epidermoid_anaplastic_occipital_oral_middle_Wilms_parietal



Phase1 CAGE Peaks

Hg19::chr11:69988499..69988503,-p@chr11:69988499..69988503
-
Hg19::chr17:39678090..39678101,-p4@KRT15
Hg19::chr19:51512580..51512608,-p@chr19:51512580..51512608
-
Hg19::chr2:72258505..72258535,+p@chr2:72258505..72258535
+
Hg19::chr3:193809263..193809278,+p1@ENST00000457815
Hg19::chr4:23975557..23975561,-p@chr4:23975557..23975561
-
Hg19::chr4:23981805..23981809,-p@chr4:23981805..23981809
-
Hg19::chr4:24010751..24010757,-p@chr4:24010751..24010757
-
Hg19::chr4:24053554..24053559,-p@chr4:24053554..24053559
-
Hg19::chr4:24055928..24055932,-p@chr4:24055928..24055932
-
Hg19::chr4:24059076..24059080,-p@chr4:24059076..24059080
-
Hg19::chr4:24105215..24105219,-p@chr4:24105215..24105219
-
Hg19::chr4:24125531..24125534,-p@chr4:24125531..24125534
-
Hg19::chr4:24188430..24188435,-p@chr4:24188430..24188435
-
Hg19::chr4:24202276..24202277,-p@chr4:24202276..24202277
-
Hg19::chr4:24208460..24208464,-p@chr4:24208460..24208464
-
Hg19::chr4:24232569..24232574,-p@chr4:24232569..24232574
-
Hg19::chr5:84943573..84943591,-p@chr5:84943573..84943591
-
Hg19::chr6:43706592..43706595,-p@chr6:43706592..43706595
-
Hg19::chr6:43706642..43706655,-p@chr6:43706642..43706655
-
Hg19::chr7:55088621..55088630,+p@chr7:55088621..55088630
+
Hg19::chr9:135687993..135687996,+p@chr9:135687993..135687996
+


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:0005200structural constituent of cytoskeleton0.0333451077357824
GO:0008544epidermis development0.0333451077357824
GO:0007398ectoderm development0.0333451077357824
GO:0045111intermediate filament cytoskeleton0.0333451077357824
GO:0005882intermediate filament0.0333451077357824
GO:0009888tissue development0.0359119274696809



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
mammalian vulva7.48e-301
external female genitalia7.48e-301
regional part of telencephalon1.23e-2132
cerebral hemisphere1.23e-2132
brain grey matter1.98e-2034
gray matter1.98e-2034
telencephalon1.98e-2034
regional part of cerebral cortex4.35e-2022
cerebral cortex7.67e-1825
pallium7.67e-1825
regional part of forebrain4.24e-1741
forebrain4.24e-1741
anterior neural tube4.24e-1741
future forebrain4.24e-1741
middle temporal gyrus1.54e-152
Ammon's horn1.78e-152
lobe parts of cerebral cortex1.78e-152
hippocampal formation1.78e-152
limbic lobe1.78e-152
caudate nucleus2.37e-152
future caudate nucleus2.37e-152
regional part of nervous system2.18e-1353
regional part of brain2.18e-1353
neocortex8.39e-1320
neural tube1.06e-1256
neural rod1.06e-1256
future spinal cord1.06e-1256
neural keel1.06e-1256
pre-chordal neural plate1.05e-1161
caudate-putamen1.09e-103
dorsal striatum1.09e-103
frontal cortex1.20e-103
brain2.09e-1068
future brain2.09e-1068
central nervous system8.05e-0981
neural plate8.05e-0982
presumptive neural plate8.05e-0982
neurectoderm1.99e-0886
corpus striatum2.43e-084
striatum2.43e-084
ventral part of telencephalon2.43e-084
future corpus striatum2.43e-084
nervous system5.54e-0889
ecto-epithelium5.06e-07104
limbic system5.70e-075
occipital lobe6.04e-075
Disease
Ontology termp-valuen
squamous cell carcinoma3.58e-0914


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)
MA0003.10.00111244
MA0004.10.478761
MA0006.10.0694838
MA0007.10.449227
MA0009.10.526253
MA0014.10.00921962
MA0017.10.297619
MA0019.10.726406
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.11.77698
MA0038.10.22896
MA0040.11.15521
MA0041.10.508527
MA0042.10.149889
MA0043.10.526535
MA0046.10.516541
MA0048.10.186532
MA0050.10.897174
MA0051.10.641247
MA0052.10.459414
MA0055.10.311622
MA0056.10
MA0057.10.0257204
MA0058.10.333443
MA0059.10.101051
MA0060.10.265848
MA0061.10.0189504
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.514926
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.0034706
MA0074.10.639966
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.11.31963
MA0084.10.999884
MA0087.10.497023
MA0088.10.270219
MA0089.10
MA0090.10.759616
MA0091.10.160096
MA0092.10.837387
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.0724124
MA0103.10.232452
MA0105.10.00342752
MA0106.12.04446
MA0107.10.162095
MA0108.20.383574
MA0109.10
MA0111.10.398557
MA0113.10.272101
MA0114.10.0401034
MA0115.10.747865
MA0116.10.166035
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.10.0745458
MA0140.10.199454
MA0141.10.100114
MA0142.10.945139
MA0143.10.272236
MA0144.10.140794
MA0145.10.0109701
MA0146.10.00192039
MA0147.10.385197
MA0148.10.99741
MA0149.10.192747
MA0062.20.0177333
MA0035.20.57743
MA0039.20.0201389
MA0138.20.302079
MA0002.20.0984982
MA0137.20.274591
MA0104.20.108753
MA0047.21.29176
MA0112.20.0833569
MA0065.20.192051
MA0150.10.115337
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.10.26587
MA0155.10.0746593
MA0156.10.277694
MA0157.10.89541
MA0158.10
MA0159.10.686643
MA0160.10.18494
MA0161.10
MA0162.10.000506716
MA0163.10.0106129
MA0164.10.770204
MA0080.20.531199
MA0018.20.260646
MA0099.20.59018
MA0079.21.88294e-05
MA0102.21.03595
MA0258.10.892318
MA0259.10.179817
MA0442.10



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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