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{{Coexpression_clusters
{
|full_id=C2275_MCF7_breast_Hepatocyte_pancreatic_liver_parietal_temporal

Latest revision as of 12:02, 17 September 2013


Full id: C2275_MCF7_breast_Hepatocyte_pancreatic_liver_parietal_temporal



Phase1 CAGE Peaks

Hg19::chr14:100437780..100437791,+p10@EVL
Hg19::chr14:100437793..100437811,+p8@EVL
Hg19::chr14:100437825..100437840,+p9@EVL
Hg19::chr14:100437931..100437940,+p17@EVL


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.72e-1856
neural rod4.72e-1856
future spinal cord4.72e-1856
neural keel4.72e-1856
regional part of nervous system2.76e-1753
regional part of brain2.76e-1753
neural plate4.86e-1682
presumptive neural plate4.86e-1682
central nervous system5.19e-1681
nervous system9.62e-1689
neurectoderm1.86e-1586
brain7.81e-1568
future brain7.81e-1568
regional part of forebrain1.00e-1441
forebrain1.00e-1441
anterior neural tube1.00e-1441
future forebrain1.00e-1441
tube1.05e-14192
structure with developmental contribution from neural crest7.75e-14132
anatomical conduit1.65e-13240
pre-chordal neural plate5.27e-1361
telencephalon9.99e-1334
anatomical cluster2.08e-12373
cerebral hemisphere2.92e-1232
brain grey matter2.95e-1234
gray matter2.95e-1234
ectoderm-derived structure3.60e-12171
ectoderm3.60e-12171
presumptive ectoderm3.60e-12171
regional part of telencephalon4.69e-1232
ecto-epithelium7.94e-12104
cell layer8.27e-12309
epithelium1.71e-11306
regional part of cerebral cortex8.99e-1122
neocortex1.02e-1020
cerebral cortex1.44e-1025
pallium1.44e-1025
adult organism1.77e-10114
multi-tissue structure6.52e-10342
organ system subdivision1.51e-07223


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)
MA0003.15.41581
MA0004.12.8475
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.14.90963
MA0059.13.65449
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.16.9203
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.13.35176
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.15.10287
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.061409
MA0147.17.75267
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.29.51044
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.27.08088
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.15.3466
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.25.41326
MA0102.21.75932
MA0258.10.418966
MA0259.15.32193
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
E2F1#186944.907389214879320.001724022357361790.0106340167127633
E2F6#187645.017155731697390.00157802193473060.00995692561873665
EGR1#195844.988179094810140.001615011500076050.0101327758053853
HEY1#2346244.040111043105710.00375304636917980.0185703515303345
MYC#460945.22228187160940.001344309395272740.00886409046864634
NRF1#4899412.21027944771094.49717228915276e-050.000792709158998861
TAF1#687243.343046285745290.008005664898701650.0321578321675193
TBP#690843.706770687096390.005296377814784350.0243731395725165
USF1#739146.361499277207960.0006105011399140830.00507280838185114
USF2#7392412.99219738506963.50833029870167e-050.000680547006066314



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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