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Coexpression cluster:C1537: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1537_clear_endometrial_serous_Neural_Fibroblast_CD14_melanoma
|id=C1537
}}

Latest revision as of 11:47, 17 September 2013


Full id: C1537_clear_endometrial_serous_Neural_Fibroblast_CD14_melanoma



Phase1 CAGE Peaks

Hg19::chr7:20370300..20370359,+p1@ITGB8
Hg19::chr7:20370483..20370513,+p3@ITGB8
Hg19::chr7:20370516..20370553,+p2@ITGB8
Hg19::chr7:20370652..20370663,+p12@ITGB8
Hg19::chr7:20370666..20370680,+p5@ITGB8
Hg19::chr7:20370694..20370705,+p15@ITGB8


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 tube1.18e-2756
neural rod1.18e-2756
future spinal cord1.18e-2756
neural keel1.18e-2756
central nervous system2.94e-2781
regional part of nervous system1.04e-2553
regional part of brain1.04e-2553
nervous system9.27e-2589
anatomical cluster2.68e-23373
brain2.73e-2368
future brain2.73e-2368
neural plate6.51e-2382
presumptive neural plate6.51e-2382
neurectoderm9.46e-2286
ectoderm-derived structure2.99e-21171
ectoderm2.99e-21171
presumptive ectoderm2.99e-21171
ecto-epithelium4.95e-21104
anatomical system5.50e-21624
multi-cellular organism5.97e-21656
anatomical group8.88e-21625
regional part of forebrain2.33e-2041
forebrain2.33e-2041
anterior neural tube2.33e-2041
future forebrain2.33e-2041
adult organism4.95e-19114
organ6.20e-19503
embryo2.25e-18592
brain grey matter2.73e-1834
gray matter2.73e-1834
telencephalon5.12e-1834
anatomical conduit9.49e-18240
developing anatomical structure4.10e-17581
regional part of telencephalon5.28e-1732
cerebral hemisphere7.93e-1732
pre-chordal neural plate2.73e-1661
organ system subdivision3.84e-16223
multi-tissue structure4.12e-16342
structure with developmental contribution from neural crest1.36e-15132
tube1.53e-14192
embryonic structure2.48e-13564
cerebral cortex3.54e-1325
pallium3.54e-1325
germ layer8.12e-13560
germ layer / neural crest8.12e-13560
embryonic tissue8.12e-13560
presumptive structure8.12e-13560
germ layer / neural crest derived structure8.12e-13560
epiblast (generic)8.12e-13560
regional part of cerebral cortex2.67e-1122
organ part9.08e-11218
epithelium2.90e-10306
neocortex4.25e-1020
cell layer1.08e-09309
posterior neural tube1.92e-0815
chordal neural plate1.92e-0815
segmental subdivision of nervous system7.32e-0713


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)
MA0003.11.73878
MA0004.10.558729
MA0006.11.01439
MA0007.11.33289
MA0009.11.03681
MA0014.12.54844
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.12.26581
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.12.69973
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.13.89731
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.18.73044
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.12.01346
MA0142.10.838805
MA0143.12.88894
MA0144.10.811435
MA0145.11.16614
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.21.87543
MA0104.20.735746
MA0047.20.695777
MA0112.24.40771
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.16.74377
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.12.08316
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.21.68161
MA0102.21.58513
MA0258.14.97441
MA0259.10.336472
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
BATF#10538312.17890089615180.00125981487125340.00846297069137669
CTCF#1066465.360256373075034.21437267579784e-050.000756392623969154
E2F1#186964.907389214879327.15746523583771e-050.00112815954084765
E2F6#187665.017155731697396.26776799983417e-050.00102537503467212
EBF1#187957.422055705474179.7002838805275e-050.00138022881225942
EGR1#195854.156815912341780.001617966818864440.0101360948110721
ESR1#2099630.76860329615451.17571957705476e-091.07711383252651e-07
FOXA1#3169611.08141974938555.39600313513231e-072.51025911550148e-05
IRF4#3662621.91451268674419.01304984425575e-096.9011283921131e-07
JUND#372744.663109294580680.004917643408260230.0229929605549219
MAX#414966.452555509007121.3848964723355e-050.000334808339523721
MXI1#460169.96157162875931.02262624227062e-064.30653476276214e-05
MYC#460965.22228187160944.92821127172503e-050.000854837164935544
NR3C1#2908614.9730233311738.86442195171695e-085.25122725022897e-06
PAX5#507966.669565531177831.13557256338955e-050.000290112678443838
POLR2A#543062.147453176558070.01019570676818780.0380758570822701
RAD21#5885610.35503389545638.10515055094479e-073.54775280129976e-05
SMARCB1#6598412.16847718743830.0001234985463193470.0016608375842192
SMARCC1#6599643.66335931963151.43811211260506e-101.52482224292751e-08
SP1#666765.69838137814092.91961319085282e-050.000610086998878508
TAF1#687263.343046285745290.0007162474284635620.00573871616273924
TBP#690863.706770687096390.000385416472907960.00378170903927419
TFAP2C#7022610.80922860986026.2644941908553e-072.86829245418122e-05
TRIM28#10155412.39368336350830.0001149534924635960.00157285835181521



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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