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Coexpression cluster:C2744: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2744_breast_Renal_mature_adipose_lung_Endothelial_heart
|id=C2744
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2744_breast_Renal_mature_adipose_lung_Endothelial_heart



Phase1 CAGE Peaks

Hg19::chr3:52479112..52479126,-p1@SEMA3G
Hg19::chr7:1094939..1094950,+p4@GPR146
Hg19::chr7:1094970..1094983,+p5@GPR146
Hg19::chr7:1094987..1095014,+p2@GPR146


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

No GOStat results

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><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.71e-75114
neural tube2.60e-2756
neural rod2.60e-2756
future spinal cord2.60e-2756
neural keel2.60e-2756
regional part of nervous system1.96e-2553
regional part of brain1.96e-2553
regional part of forebrain2.51e-2141
forebrain2.51e-2141
anterior neural tube2.51e-2141
future forebrain2.51e-2141
neural plate6.54e-2182
presumptive neural plate6.54e-2182
neurectoderm9.41e-2186
brain grey matter1.23e-1834
gray matter1.23e-1834
telencephalon1.91e-1834
brain5.56e-1868
future brain5.56e-1868
central nervous system1.21e-1781
regional part of telencephalon4.25e-1732
cerebral hemisphere5.64e-1732
nervous system3.11e-1689
regional part of cerebral cortex4.52e-1522
pre-chordal neural plate7.33e-1561
ecto-epithelium2.76e-14104
neocortex6.75e-1420
anatomical conduit1.09e-13240
tube6.28e-13192
structure with developmental contribution from neural crest2.15e-12132
cerebral cortex2.16e-1225
pallium2.16e-1225
anatomical cluster4.84e-11373
organ system subdivision5.72e-09223
neural nucleus5.54e-089
nucleus of brain5.54e-089
ectoderm-derived structure5.96e-08171
ectoderm5.96e-08171
presumptive ectoderm5.96e-08171
basal ganglion1.04e-079
nuclear complex of neuraxis1.04e-079
aggregate regional part of brain1.04e-079
collection of basal ganglia1.04e-079
cerebral subcortex1.04e-079
blood vessel endothelium1.91e-0718
endothelium1.91e-0718
cardiovascular system endothelium1.91e-0718
posterior neural tube3.36e-0715
chordal neural plate3.36e-0715


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)
MA0003.11.8989
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.12.36201
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.12.95284
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.13.05944
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.12.92476
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.21.83323
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.24.98884
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.13.66667
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.11.07498
MA0259.11.1888
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90534.752151182721970.01386206996689490.0487372740371161
E2F6#187645.017155731697390.00157802193473060.00998346455302453
GABPB1#255335.300762877136630.01012678824234270.0378767194514211
GATA1#2623310.17023110785030.001515158168498270.00966715156452998
GATA2#262439.55869880016550.001818151618357440.0109048375851164
HMGN3#932436.133910792512940.006640696683324720.0283080702412143
NRF1#489939.157709585783180.002061953791733420.0119651290173823
TAL1#6886322.40146250808020.0001462756395930170.00188953389282067
TRIM28#10155313.94289378394690.0005972858184258420.0049955901009511



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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