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Coexpression cluster:C2516: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2516_Placental_cerebral_Wilms_hippocampus_amygdala_Bronchial_mesothelioma
|id=C2516
|ontology_enrichment_celltype=CL:0000066!3.59e-13!254;CL:0002076!6.78e-09!43;CL:0000223!2.91e-08!59;CL:0002368!2.76e-07!13
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003075!2.28e-27!86;UBERON:0007284!2.28e-27!86;UBERON:0001049!2.52e-26!57;UBERON:0005068!2.52e-26!57;UBERON:0006241!2.52e-26!57;UBERON:0007135!2.52e-26!57;UBERON:0007023!6.19e-26!115;UBERON:0002346!4.86e-25!90;UBERON:0002616!2.26e-22!59;UBERON:0004121!8.50e-21!169;UBERON:0003080!3.44e-20!42;UBERON:0002780!6.09e-20!41;UBERON:0001890!6.09e-20!41;UBERON:0006240!6.09e-20!41;UBERON:0000481!7.67e-20!347;UBERON:0005743!1.00e-19!86;UBERON:0000033!1.17e-19!123;UBERON:0003056!1.24e-19!61;UBERON:0000924!1.39e-19!173;UBERON:0006601!1.39e-19!173;UBERON:0000153!2.25e-19!129;UBERON:0007811!2.25e-19!129;UBERON:0000064!3.75e-19!219;UBERON:0001017!9.89e-19!82;UBERON:0000955!2.57e-17!69;UBERON:0006238!2.57e-17!69;UBERON:0000477!7.32e-17!286;UBERON:0004111!8.58e-17!241;UBERON:0002020!1.07e-16!34;UBERON:0003528!1.07e-16!34;UBERON:0001893!1.75e-16!34;UBERON:0000483!2.78e-16!309;UBERON:0002791!6.50e-16!33;UBERON:0000073!2.12e-15!94;UBERON:0001016!2.12e-15!94;UBERON:0000119!2.45e-15!312;UBERON:0001869!2.68e-15!32;UBERON:0000922!3.86e-14!612;UBERON:0000025!4.13e-14!194;UBERON:0000062!9.20e-14!511;UBERON:0002619!2.59e-12!22;UBERON:0002050!3.26e-12!605;UBERON:0005423!3.26e-12!605;UBERON:0000923!3.59e-12!604;UBERON:0005291!3.59e-12!604;UBERON:0006598!3.59e-12!604;UBERON:0002532!3.59e-12!604;UBERON:0000475!1.04e-11!365;UBERON:0000956!1.70e-11!25;UBERON:0000203!1.70e-11!25;UBERON:0001950!5.12e-11!20;UBERON:0000468!1.64e-10!659;UBERON:0000467!2.81e-10!625;UBERON:0000480!4.69e-10!626;UBERON:0004119!1.17e-09!169;UBERON:0000925!1.17e-09!169;UBERON:0006595!1.17e-09!169;UBERON:0000063!5.67e-08!97;UBERON:0003076!2.56e-07!15;UBERON:0003057!2.56e-07!15;UBERON:0004921!3.52e-07!129;UBERON:0004185!3.52e-07!129;UBERON:0002308!7.93e-07!9;UBERON:0000125!7.93e-07!9;UBERON:0001007!9.31e-07!155;UBERON:0001555!9.31e-07!155;UBERON:0007026!9.31e-07!155;UBERON:0001004!9.87e-07!72
}}

Latest revision as of 12:07, 17 September 2013


Full id: C2516_Placental_cerebral_Wilms_hippocampus_amygdala_Bronchial_mesothelioma



Phase1 CAGE Peaks

Hg19::chr1:11714406..11714429,-p2@FBXO2
Hg19::chr1:11714446..11714457,-p4@FBXO2
Hg19::chr1:11714462..11714471,-p7@FBXO2
Hg19::chr1:11714479..11714493,-p1@FBXO2


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
epithelial cell1.51e-11253
endo-epithelial cell2.58e-0842
endodermal cell1.67e-0758
respiratory epithelial cell4.49e-0713
Uber Anatomy
Ontology termp-valuen
ecto-epithelium9.15e-29104
neural tube1.11e-2756
neural rod1.11e-2756
future spinal cord1.11e-2756
neural keel1.11e-2756
neural plate2.27e-2782
presumptive neural plate2.27e-2782
adult organism1.69e-26114
regional part of nervous system1.09e-2553
regional part of brain1.09e-2553
neurectoderm3.91e-2586
organ system subdivision1.01e-22223
anatomical cluster2.58e-22373
multi-tissue structure2.97e-22342
regional part of forebrain4.96e-2141
forebrain4.96e-2141
anterior neural tube4.96e-2141
future forebrain4.96e-2141
pre-chordal neural plate5.92e-2161
ectoderm-derived structure3.90e-20171
ectoderm3.90e-20171
presumptive ectoderm3.90e-20171
central nervous system3.46e-1981
organ part3.51e-19218
brain1.78e-1868
future brain1.78e-1868
anatomical conduit1.12e-17240
brain grey matter1.28e-1734
gray matter1.28e-1734
telencephalon1.79e-1734
structure with developmental contribution from neural crest3.22e-17132
regional part of telencephalon2.70e-1632
cerebral hemisphere2.75e-1632
epithelium4.23e-16306
organ2.01e-15503
cell layer3.55e-15309
nervous system1.14e-1489
tube3.82e-14192
regional part of cerebral cortex4.35e-1322
embryo4.66e-13592
cerebral cortex3.91e-1225
pallium3.91e-1225
developing anatomical structure4.54e-12581
neocortex8.72e-1220
embryonic structure4.89e-11564
anatomical system5.70e-11624
anatomical group9.55e-11625
multi-cellular organism1.59e-10656
germ layer3.88e-10560
germ layer / neural crest3.88e-10560
embryonic tissue3.88e-10560
presumptive structure3.88e-10560
germ layer / neural crest derived structure3.88e-10560
epiblast (generic)3.88e-10560
endoderm-derived structure4.36e-10160
endoderm4.36e-10160
presumptive endoderm4.36e-10160
posterior neural tube8.19e-0815
chordal neural plate8.19e-0815
neural nucleus4.13e-079
nucleus of brain4.13e-079
digestive system4.86e-07145
digestive tract4.86e-07145
primitive gut4.86e-07145
basal ganglion5.03e-079
nuclear complex of neuraxis5.03e-079
aggregate regional part of brain5.03e-079
collection of basal ganglia5.03e-079
cerebral subcortex5.03e-079
organ segment5.33e-0798
subdivision of digestive tract5.65e-07118


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)
MA0003.14.74396
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.18.67501
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.16.9203
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.07281
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.12.44319
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.24.29465
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.23.96014
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.43857
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
HEY1#2346244.040111043105710.00375304636917980.0186109116257903
REST#597849.650028716128020.0001152825614219170.00157036591004873
SP1#666745.69838137814090.0009482606065333980.00684276856807445
TAF1#687243.343046285745290.008005664898701650.0322322142002892
ZBTB7A#5134147.35190930787590.000342223540015990.0034663450970546



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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