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Coexpression cluster:C3805: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3805_Mammary_skeletal_Mesenchymal_Osteoblast_Corneal_Pericytes_Fibroblast
|id=C3805
}}

Latest revision as of 12:33, 17 September 2013


Full id: C3805_Mammary_skeletal_Mesenchymal_Osteoblast_Corneal_Pericytes_Fibroblast



Phase1 CAGE Peaks

Hg19::chr19:46916678..46916710,-p3@CCDC8
Hg19::chr19:46916779..46916800,-p4@CCDC8
Hg19::chr19:46916805..46916852,-p1@CCDC8


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
multi-tissue structure4.46e-14342
compound organ6.02e-1468
organism subdivision7.73e-14264
multi-cellular organism1.05e-12656
mesenchyme6.07e-11160
entire embryonic mesenchyme6.07e-11160
cell layer2.53e-10309
epithelium1.38e-09306
anatomical system2.47e-08624
multilaminar epithelium2.91e-0883
trunk3.30e-08199
anatomical group3.65e-08625
epithelial vesicle5.45e-0878
embryo5.58e-08592
primary circulatory organ7.23e-0827
urinary system structure7.30e-0847
muscle tissue7.35e-0864
musculature7.35e-0864
musculature of body7.35e-0864
skeletal muscle tissue7.47e-0862
striated muscle tissue7.47e-0862
myotome7.47e-0862
renal system1.18e-0748
dense mesenchyme tissue2.43e-0773
anatomical cluster3.54e-07373
somite4.46e-0771
presomitic mesoderm4.46e-0771
presumptive segmental plate4.46e-0771
dermomyotome4.46e-0771
trunk paraxial mesoderm4.46e-0771
paraxial mesoderm4.52e-0772
presumptive paraxial mesoderm4.52e-0772


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)
MA0003.13.8806
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
MA0072.11.29561
MA0073.10.0185922
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
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
MA0141.12.84752
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.13.85295
MA0146.17.1063
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.74132
MA0138.22.38017
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.12.83144
MA0156.12.7096
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
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
CCNT2#90536.336201576962630.003930750035764890.0190013239058204
CHD2#1106310.34402283411690.0009033701102746880.00660370063323148
E2F4#1874312.66806031528440.0004917987006298980.00437131612724136
E2F6#187635.017155731697390.00791769806886330.0322183615917562
EGR1#195834.988179094810140.008056488137383440.0320586590177623
ELF1#199734.258097958807540.01295179875054610.0462246833786106
ESR1#2099330.76860329615453.43136389821584e-050.000676421695292118
ETS1#211339.728760922202340.001085840092584840.00762175236437044
FOS#235338.99795530889440.001372499272417130.00897348513283915
GABPB1#255337.067683836182170.002832212825417420.0154083177201526
GTF2F1#2962312.73966087675770.0004835525047438590.00433863746073401
HMGN3#932438.178547723350590.001827766942164210.0108694995827747
IRF1#365937.63716375356390.002244692747297240.0128063730927006
JUND#372736.994663941871030.002921845042734990.0156770909025533
NFYA#4800318.42558069983050.0001598135507814160.00199626449348886
NFYB#4801316.75979325353650.0002123649923296180.0024580724186981
REST#597839.650028716128020.001112636247114590.00767419211546696
SIN3A#2594235.408884726815140.006318961977991520.0276730153480148
SP1#666735.69838137814090.005403962701712170.0246477622763611
SP2#6668326.15353049384465.58768218891694e-050.000940032120052023
SPI1#668838.204323508522730.001810593189410520.0109077377773907
TAF7#6879311.43306940492390.0006690181981945830.00542944996512892
YY1#752834.911170749853860.008441455341808260.0329367188868051
ZBTB7A#5134137.35190930787590.002516255860282270.0140172416146799



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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