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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:32, 17 September 2013


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)
MA0003.10.115024
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.954641
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.11.76197
MA0030.11.73868
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.11.02846
MA0042.11.71387
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.14.21299
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.575522
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.55119
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.602634
MA0146.10.0169564
MA0147.10.184931
MA0148.10.403564
MA0149.18.72292
MA0062.20.114378
MA0035.20.437071
MA0039.20.360905
MA0138.20.569505
MA0002.20.129981
MA0137.20.710884
MA0104.20.138396
MA0047.20.504873
MA0112.20.904106
MA0065.20.0371828
MA0150.10.315136
MA0151.10
MA0152.11.12912
MA0153.10.926242
MA0154.10.185581
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.00405048
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.300798
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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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