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Coexpression cluster:C4291: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4291_pleomorphic_Cardiac_breast_aorta_lung_diaphragm_mesothelioma
|id=C4291
|ontology_enrichment_celltype=CL:0000057!1.21e-07!75;CL:0000055!1.40e-07!180
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.36e-33!115;UBERON:0000477!1.35e-26!286;UBERON:0004111!9.86e-23!241;UBERON:0000468!2.42e-19!659;UBERON:0000025!4.96e-19!194;UBERON:0002616!1.44e-18!59;UBERON:0001049!2.36e-18!57;UBERON:0005068!2.36e-18!57;UBERON:0006241!2.36e-18!57;UBERON:0007135!2.36e-18!57;UBERON:0000475!2.90e-18!365;UBERON:0000955!1.09e-16!69;UBERON:0006238!1.09e-16!69;UBERON:0000481!2.65e-16!347;UBERON:0001017!3.01e-16!82;UBERON:0005743!1.92e-15!86;UBERON:0000119!7.56e-15!312;UBERON:0000483!1.10e-14!309;UBERON:0002346!2.45e-14!90;UBERON:0003075!4.63e-14!86;UBERON:0007284!4.63e-14!86;UBERON:0000467!1.54e-13!625;UBERON:0000480!2.00e-13!626;UBERON:0000073!2.51e-13!94;UBERON:0001016!2.51e-13!94;UBERON:0003080!4.55e-13!42;UBERON:0002780!1.81e-12!41;UBERON:0001890!1.81e-12!41;UBERON:0006240!1.81e-12!41;UBERON:0000033!1.64e-11!123;UBERON:0000153!3.87e-11!129;UBERON:0007811!3.87e-11!129;UBERON:0002020!3.11e-10!34;UBERON:0003528!3.11e-10!34;UBERON:0000924!3.50e-10!173;UBERON:0006601!3.50e-10!173;UBERON:0001893!6.46e-10!34;UBERON:0004121!7.58e-10!169;UBERON:0000922!8.62e-10!612;UBERON:0002791!1.07e-09!33;UBERON:0002050!1.15e-09!605;UBERON:0005423!1.15e-09!605;UBERON:0004872!1.36e-09!84;UBERON:0000062!2.07e-09!511;UBERON:0000923!2.53e-09!604;UBERON:0005291!2.53e-09!604;UBERON:0006598!2.53e-09!604;UBERON:0002532!2.53e-09!604;UBERON:0001869!3.89e-09!32;UBERON:0002049!4.96e-08!79;UBERON:0007798!4.96e-08!79;UBERON:0003056!1.20e-07!61;UBERON:0001009!1.59e-07!113;UBERON:0003914!2.34e-07!118;UBERON:0004535!2.35e-07!110;UBERON:0002619!2.74e-07!22;UBERON:0000055!3.33e-07!69
}}

Latest revision as of 12:43, 17 September 2013


Full id: C4291_pleomorphic_Cardiac_breast_aorta_lung_diaphragm_mesothelioma



Phase1 CAGE Peaks

Hg19::chr3:145968857..145968899,-p1@PLSCR4
Hg19::chr3:145968900..145968915,-p3@PLSCR4
Hg19::chr3:145968923..145968935,-p4@PLSCR4


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>

Cell Type
Ontology termp-valuen
fibroblast4.12e-0876
Uber Anatomy
Ontology termp-valuen
adult organism6.37e-32114
anatomical cluster3.31e-22373
anatomical conduit4.04e-20240
multi-cellular organism1.60e-17656
multi-tissue structure4.79e-17342
neural tube6.98e-1756
neural rod6.98e-1756
future spinal cord6.98e-1756
neural keel6.98e-1756
tube8.40e-17192
structure with developmental contribution from neural crest5.77e-16132
brain1.62e-1568
future brain1.62e-1568
central nervous system3.79e-1581
regional part of nervous system4.20e-1553
regional part of brain4.20e-1553
cell layer5.02e-13309
epithelium6.23e-13306
nervous system7.11e-1389
neurectoderm3.10e-1286
organ system subdivision3.92e-12223
anatomical system4.79e-12624
neural plate5.57e-1282
presumptive neural plate5.57e-1282
anatomical group6.04e-12625
regional part of forebrain6.55e-1241
forebrain6.55e-1241
anterior neural tube6.55e-1241
future forebrain6.55e-1241
brain grey matter7.75e-1034
gray matter7.75e-1034
ectoderm-derived structure1.07e-09171
ectoderm1.07e-09171
presumptive ectoderm1.07e-09171
telencephalon1.77e-0934
germ layer4.32e-09560
germ layer / neural crest4.32e-09560
embryonic tissue4.32e-09560
presumptive structure4.32e-09560
germ layer / neural crest derived structure4.32e-09560
epiblast (generic)4.32e-09560
embryonic structure7.35e-09564
regional part of telencephalon7.53e-0932
cerebral hemisphere9.10e-0932
organ1.39e-08503
ecto-epithelium1.62e-08104
splanchnic layer of lateral plate mesoderm1.95e-0883
embryo1.03e-07592
developing anatomical structure1.08e-07581
regional part of cerebral cortex6.26e-0722


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
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.14.47204
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.12.15619
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
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
MA0081.10.714712
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
MA0105.10.846801
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
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.15.73745
MA0145.10.752137
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.16.40038
MA0062.21.141
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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
E2F1#186934.907389214879320.008460985347239390.0326566705599
GATA1#2623313.56030814380040.0004009615963782630.00388712783478599
STAT1#6772320.70658749719920.0001125992441046670.00155121388405847
STAT3#6774310.51946499715420.0008589184530415310.0064433690789545
TFAP2A#7020316.5186343730450.0002218033880766340.00248924608288584



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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