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Coexpression cluster:C4534: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4534_skeletal_squamous_amniotic_heart_left_mesothelioma_somatostatinoma
|id=C4534
}}

Latest revision as of 14:14, 17 September 2013


Full id: C4534_skeletal_squamous_amniotic_heart_left_mesothelioma_somatostatinoma



Phase1 CAGE Peaks

Hg19::chr5:96038476..96038517,+p1@CAST
Hg19::chr5:96038525..96038547,+p6@CAST
Hg19::chr5:96038554..96038572,+p11@CAST


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
organ1.66e-09503
endoderm-derived structure6.59e-08160
endoderm6.59e-08160
presumptive endoderm6.59e-08160
multi-cellular organism3.53e-07656
digestive system3.86e-07145
digestive tract3.86e-07145
primitive gut3.86e-07145
anatomical system7.10e-07624
Disease
Ontology termp-valuen
cell type cancer1.35e-07143


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)
MA0003.10.708947
MA0004.11.93041
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.19.33321
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
MA0058.14.13609
MA0059.16.94978
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.12.97077
MA0091.10.829044
MA0092.11.84783
MA0093.12.626
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
MA0111.11.80901
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
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.107247
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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#90536.336201576962630.003930750035764890.0190923450369849
CEBPB#105137.971147625824820.001974187055288560.011567019459595
E2F6#187635.017155731697390.00791769806886330.0323963356949663
EGR1#195834.988179094810140.008056488137383440.0322133064540654
ETS1#211339.728760922202340.001085840092584840.00764590435743445
FOS#235338.99795530889440.001372499272417130.00901184782547294
FOSL1#8061339.7135797163731.59554825631833e-050.00037237422199247
GABPB1#255337.067683836182170.002832212825417420.0154711792077917
GTF2F1#2962312.73966087675770.0004835525047438590.00435773061031529
HDAC2#3066313.41562023662630.0004140761399857210.0039310697194772
HMGN3#932438.178547723350590.001827766942164210.0109086320174118
JUNB#3726330.61063265982113.4847716247536e-050.000682057840550303
JUND#372736.994663941871030.002921845042734990.0157515394837248
MAX#414936.452555509007120.003721913834265510.018727739397613
MXI1#460139.96157162875930.001011470541259020.00722748849606944
MYC#460935.22228187160940.007020843755740150.029578455062757
SIN3A#2594235.408884726815140.006318961977991520.0278012498955033
SMARCB1#6598318.25271578115740.000164397760679890.00203865325666671
STAT3#6774310.51946499715420.0008589184530415310.00645078270654426
USF1#739136.361499277207960.00388404057290560.0191008764605965
USF2#7392312.99219738506960.0004558979393427810.00422742829503869
YY1#752834.911170749853860.008441455341808260.0330937370286454
ZEB1#6935316.88843201754390.0002075486917327580.00243662070772004
ZNF263#1012738.221841637010680.001799043925565870.0109980302354352



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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