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{{Coexpression_clusters
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|full_id=C3971_Mast_breast_lung_Wilms_salivary_mesothelioma_oral
|id=C3971
|ontology_enrichment_celltype=CL:0000066!9.93e-20!254;CL:0002076!2.67e-10!43;CL:0002368!5.14e-07!13;CL:0000076!7.81e-07!62
|ontology_enrichment_disease=DOID:0050687!2.36e-10!143;DOID:305!1.13e-09!106;DOID:299!6.31e-08!25;DOID:1749!9.15e-08!14
|ontology_enrichment_uberon=UBERON:0004121!1.82e-18!169;UBERON:0000924!2.69e-18!173;UBERON:0006601!2.69e-18!173;UBERON:0000153!2.45e-15!129;UBERON:0007811!2.45e-15!129;UBERON:0000033!3.23e-15!123;UBERON:0005743!3.65e-14!86;UBERON:0003075!1.36e-13!86;UBERON:0007284!1.36e-13!86;UBERON:0001017!1.48e-13!82;UBERON:0000464!2.16e-13!104;UBERON:0003056!2.87e-13!61;UBERON:0002346!2.94e-13!90;UBERON:0000073!1.53e-12!94;UBERON:0001016!1.53e-12!94;UBERON:0000475!5.42e-12!365;UBERON:0001049!5.95e-12!57;UBERON:0005068!5.95e-12!57;UBERON:0006241!5.95e-12!57;UBERON:0007135!5.95e-12!57;UBERON:0000955!7.33e-12!69;UBERON:0006238!7.33e-12!69;UBERON:0002616!2.11e-11!59;UBERON:0001869!3.45e-11!32;UBERON:0003080!5.61e-11!42;UBERON:0002780!8.82e-11!41;UBERON:0001890!8.82e-11!41;UBERON:0006240!8.82e-11!41;UBERON:0001893!1.32e-10!34;UBERON:0000064!1.49e-10!219;UBERON:0002020!2.09e-10!34;UBERON:0003528!2.09e-10!34;UBERON:0002791!3.42e-10!33;UBERON:0002619!5.59e-10!22;UBERON:0000466!9.55e-10!126;UBERON:0000481!1.04e-09!347;UBERON:0000956!1.34e-09!25;UBERON:0000203!1.34e-09!25;UBERON:0007023!1.53e-09!115;UBERON:0000062!1.88e-09!511;UBERON:0001950!1.94e-09!20;UBERON:0002553!2.60e-08!70;UBERON:0004119!7.65e-08!169;UBERON:0000925!7.65e-08!169;UBERON:0006595!7.65e-08!169;UBERON:0005156!1.12e-07!59;UBERON:0000990!1.12e-07!59;UBERON:0000119!1.91e-07!312;UBERON:0000483!2.15e-07!309;UBERON:0000922!2.64e-07!612;UBERON:0003133!2.98e-07!48;UBERON:0005177!9.18e-07!107
}}

Latest revision as of 12:36, 17 September 2013


Full id: C3971_Mast_breast_lung_Wilms_salivary_mesothelioma_oral



Phase1 CAGE Peaks

Hg19::chr1:33219558..33219569,+p5@KIAA1522
Hg19::chr1:33219575..33219586,+p4@KIAA1522
Hg19::chr1:33219592..33219626,+p1@KIAA1522


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell4.15e-22253
endo-epithelial cell1.15e-1042
endodermal cell4.08e-0758
respiratory epithelial cell6.34e-0713
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure6.01e-17171
ectoderm6.01e-17171
presumptive ectoderm6.01e-17171
central nervous system2.25e-1581
ecto-epithelium1.00e-14104
regional part of nervous system2.58e-1453
regional part of brain2.58e-1453
neural tube5.00e-1456
neural rod5.00e-1456
future spinal cord5.00e-1456
neural keel5.00e-1456
brain8.61e-1468
future brain8.61e-1468
pre-chordal neural plate9.98e-1461
nervous system2.23e-1389
organ system subdivision2.88e-13223
cerebral hemisphere3.78e-1332
neural plate4.01e-1382
presumptive neural plate4.01e-1382
neurectoderm1.14e-1286
regional part of forebrain1.61e-1241
forebrain1.61e-1241
anterior neural tube1.61e-1241
future forebrain1.61e-1241
telencephalon2.68e-1234
brain grey matter3.19e-1234
gray matter3.19e-1234
regional part of telencephalon7.81e-1232
organ part1.13e-11218
anatomical space1.75e-1195
regional part of cerebral cortex2.48e-1122
cerebral cortex5.07e-1125
pallium5.07e-1125
organ5.89e-11503
neocortex9.59e-1120
adult organism1.19e-09114
renal system1.39e-0848
urinary system structure3.17e-0847
anatomical cluster5.71e-08373
immaterial anatomical entity1.02e-07117
trunk region element1.07e-07101
thoracic cavity element1.65e-0734
thoracic cavity1.65e-0734
epithelial bud2.90e-0737
structure with developmental contribution from neural crest2.92e-07132
multi-tissue structure3.45e-07342
thoracic segment organ5.21e-0735
lung9.78e-0722
respiratory tube9.78e-0722
respiration organ9.78e-0722
pair of lungs9.78e-0722
lung primordium9.78e-0722
lung bud9.78e-0722
Disease
Ontology termp-valuen
cell type cancer8.55e-14143
carcinoma1.68e-13106
cancer1.31e-08235
disease of cellular proliferation3.50e-08239
adenocarcinoma4.48e-0825
squamous cell carcinoma5.70e-0814


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)
MA0003.16.06693
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0060.12.13518
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0114.11.35563
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
MA0144.10.531867
MA0145.10.752137
MA0146.13.73313
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.25.50873
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
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
MA0162.11.43223
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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#90536.336201576962630.003930750035764890.0190224550755409
E2F1#186934.907389214879320.008460985347239390.0325664055679345
EGR1#195834.988179094810140.008056488137383440.0320941207834683
HMGN3#932438.178547723350590.001827766942164210.0108812718276628
IRF1#365937.63716375356390.002244692747297240.0128203798444152
MYC#460935.22228187160940.007020843755740150.0294809384450686
NFYB#4801316.75979325353650.0002123649923296180.00246079967091013
SP1#666735.69838137814090.005403962701712170.0246790179108888
TAF7#6879311.43306940492390.0006690181981945830.00543663177725211
USF1#739136.361499277207960.00388404057290560.0190470635955152
USF2#7392312.99219738506960.0004558979393427810.00421956087265338
ZBTB7A#5134137.35190930787590.002516255860282270.0140352085981638



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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