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Coexpression cluster:C3301: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3301_Renal_Placental_Mesenchymal_Pericytes_Osteoblast_Astrocyte_Nucleus
|id=C3301
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3301_Renal_Placental_Mesenchymal_Pericytes_Osteoblast_Astrocyte_Nucleus



Phase1 CAGE Peaks

Hg19::chr12:56546363..56546397,+p1@MYL6B
Hg19::chr19:50354393..50354422,+p1@PTOV1
Hg19::chr19:50354430..50354447,+p2@PTOV1


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:0030049muscle filament sliding0.0107137600063315
GO:0033275actin-myosin filament sliding0.0107137600063315
GO:0016461unconventional myosin complex0.0107137600063315
GO:0030048actin filament-based movement0.0183640125820119
GO:0005859muscle myosin complex0.0198914181804517
GO:0016460myosin II complex0.0198914181804517
GO:0008307structural constituent of muscle0.0275354752527976
GO:0044449contractile fiber part0.0307366264913492
GO:0043292contractile fiber0.0307366264913492
GO:0007519skeletal muscle development0.0307366264913492
GO:0014706striated muscle development0.03668909487398
GO:0016459myosin complex0.0408816032450061



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
cell layer7.76e-32309
epithelium2.07e-31306
anatomical cluster6.25e-29373
multi-tissue structure7.10e-25342
tube5.64e-21192
anatomical conduit1.63e-19240
epithelial vesicle1.43e-1678
mesenchyme3.94e-16160
entire embryonic mesenchyme3.94e-16160
vasculature2.62e-1578
vascular system2.62e-1578
epithelial tube5.01e-15117
structure with developmental contribution from neural crest5.23e-15132
ectoderm-derived structure9.15e-15171
ectoderm9.15e-15171
presumptive ectoderm9.15e-15171
unilaminar epithelium1.27e-14148
neurectoderm2.16e-1486
dense mesenchyme tissue2.60e-1473
paraxial mesoderm3.94e-1472
presumptive paraxial mesoderm3.94e-1472
somite8.73e-1471
presomitic mesoderm8.73e-1471
presumptive segmental plate8.73e-1471
dermomyotome8.73e-1471
trunk paraxial mesoderm8.73e-1471
trunk mesenchyme1.50e-13122
splanchnic layer of lateral plate mesoderm1.73e-1383
neural plate2.06e-1382
presumptive neural plate2.06e-1382
multilaminar epithelium3.63e-1383
multi-cellular organism1.77e-12656
skeletal muscle tissue2.47e-1262
striated muscle tissue2.47e-1262
myotome2.47e-1262
central nervous system5.64e-1281
ecto-epithelium6.25e-12104
organ part6.77e-12218
epithelial tube open at both ends9.60e-1259
blood vessel9.60e-1259
blood vasculature9.60e-1259
vascular cord9.60e-1259
vessel1.27e-1168
pre-chordal neural plate1.53e-1161
organism subdivision1.61e-11264
muscle tissue3.21e-1164
musculature3.21e-1164
musculature of body3.21e-1164
nervous system4.27e-1189
embryo6.74e-11592
artery1.06e-1042
arterial blood vessel1.06e-1042
arterial system1.06e-1042
brain7.39e-1068
future brain7.39e-1068
cardiovascular system1.08e-09109
circulatory system1.26e-09112
trunk1.39e-09199
anatomical system1.77e-09624
developing anatomical structure1.83e-09581
anatomical group2.47e-09625
regional part of nervous system9.73e-0953
regional part of brain9.73e-0953
neural tube1.71e-0856
neural rod1.71e-0856
future spinal cord1.71e-0856
neural keel1.71e-0856
germ layer2.74e-08560
germ layer / neural crest2.74e-08560
embryonic tissue2.74e-08560
presumptive structure2.74e-08560
germ layer / neural crest derived structure2.74e-08560
epiblast (generic)2.74e-08560
embryonic structure6.11e-08564
systemic artery1.28e-0733
systemic arterial system1.28e-0733
organ system subdivision1.99e-07223
telencephalon3.40e-0734
brain grey matter4.25e-0734
gray matter4.25e-0734
regional part of forebrain7.77e-0741
forebrain7.77e-0741
anterior neural tube7.77e-0741
future forebrain7.77e-0741


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.14.34338
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BRCA1#672213.45615376214920.007119807716084560.0296119468782667
CCNT2#90536.336201576962630.003930750035764890.0189469517231388
E2F1#186934.907389214879320.008460985347239390.032412311509384
E2F6#187635.017155731697390.00791769806886330.0320970565778059
EGR1#195834.988179094810140.008056488137383440.0319491025432939
EP300#203336.77394172622320.003216880500103790.0167048420122484
FOXA1#3169311.08141974938550.000734755275698670.00580023478750516
HMGN3#932438.178547723350590.001827766942164210.0108447989815185
IRF1#365937.63716375356390.002244692747297240.0127756657130778
JUND#372736.994663941871030.002921845042734990.0156329187714242
MYC#460935.22228187160940.007020843755740150.0293558291698993
PAX5#507936.669565531177830.003370290999677260.0172484844276618
SIN3A#2594235.408884726815140.006318961977991520.0275770368985607
SIX5#147912317.0867153554590.0002004060546325010.0023917504216391
SP1#666735.69838137814090.005403962701712170.0245726428336867
SRF#6722313.79717826216780.0003806615025800190.00374173239227808
THAP1#55145220.91276306856750.002983447413736940.0158625599166763
USF1#739136.361499277207960.00388404057290560.0189722329822594
ZBTB7A#5134137.35190930787590.002516255860282270.0139777270247338



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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