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Coexpression cluster:C3937: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3937_Mesenchymal_Renal_Alveolar_Pericytes_Placental_Fibroblast_Osteoblast
|id=C3937
}}

Latest revision as of 12:36, 17 September 2013


Full id: C3937_Mesenchymal_Renal_Alveolar_Pericytes_Placental_Fibroblast_Osteoblast



Phase1 CAGE Peaks

Hg19::chr1:2126156..2126167,-p3@C1orf86
Hg19::chr1:2126174..2126190,-p2@C1orf86
Hg19::chr1:2126192..2126218,-p1@C1orf86


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
mesenchyme1.86e-17160
entire embryonic mesenchyme1.86e-17160
organism subdivision5.72e-16264
trunk7.65e-16199
epithelial vesicle5.32e-1578
trunk mesenchyme2.76e-14122
multilaminar epithelium8.39e-1483
unilaminar epithelium1.36e-13148
somite2.93e-1271
presomitic mesoderm2.93e-1271
presumptive segmental plate2.93e-1271
dermomyotome2.93e-1271
trunk paraxial mesoderm2.93e-1271
dense mesenchyme tissue3.79e-1273
cell layer4.99e-12309
vasculature9.68e-1278
vascular system9.68e-1278
epithelium9.73e-12306
paraxial mesoderm9.95e-1272
presumptive paraxial mesoderm9.95e-1272
epithelial tube1.15e-11117
skeletal muscle tissue5.83e-1162
striated muscle tissue5.83e-1162
myotome5.83e-1162
muscle tissue3.68e-1064
musculature3.68e-1064
musculature of body3.68e-1064
epithelial tube open at both ends2.62e-0959
blood vessel2.62e-0959
blood vasculature2.62e-0959
vascular cord2.62e-0959
splanchnic layer of lateral plate mesoderm4.08e-0983
artery7.71e-0942
arterial blood vessel7.71e-0942
arterial system7.71e-0942
multi-tissue structure8.29e-09342
vessel1.20e-0868
subdivision of trunk2.21e-07112
urinary system structure2.70e-0747
anatomical cluster3.45e-07373
renal system3.89e-0748


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)
MA0003.111.2405
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.16.45108
MA0017.11.64148
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.14.06645
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.14.54482
MA0074.10.935474
MA0076.10.734647
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
MA0105.17.43664
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.15.93331
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.114.2584
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.213.5433
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.17.07944
MA0163.19.44515
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.213.0679
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
CCNT2#90536.336201576962630.003930750035764890.0190154061320695
CTCF#1066435.360256373075030.0064925092527670.0279628509979683
E2F1#186934.907389214879320.008460985347239390.0325580062886531
E2F6#187635.017155731697390.00791769806886330.0322460017397447
EGR1#195834.988179094810140.008056488137383440.0320855538659316
ELF1#199734.258097958807540.01295179875054610.0462610434236759
ELK4#2005316.2356816584680.0002336043955745990.002557916698408
ETS1#211339.728760922202340.001085840092584840.00762790431354461
GABPB1#255337.067683836182170.002832212825417420.015421170704018
HMGN3#932438.178547723350590.001827766942164210.0108775515227471
REST#597839.650028716128020.001112636247114590.0076807863713663
SIN3A#2594235.408884726815140.006318961977991520.027698567532085
SP1#666735.69838137814090.005403962701712170.024672544725863
SPI1#668838.204323508522730.001810593189410520.0109115142590216
THAP1#55145331.36914460285133.23800758564397e-050.000647099644540893
YY1#752834.911170749853860.008441455341808260.0329638120935918
ZBTB7A#5134137.35190930787590.002516255860282270.0140314616793219



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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