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Coexpression cluster:C4213: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4213_Placental_Alveolar_Mesenchymal_Endothelial_substantia_optic_Adipocyte
|id=C4213
}}

Latest revision as of 12:41, 17 September 2013


Full id: C4213_Placental_Alveolar_Mesenchymal_Endothelial_substantia_optic_Adipocyte



Phase1 CAGE Peaks

Hg19::chr2:242498138..242498179,+p1@BOK
Hg19::chr2:242498294..242498391,+p2@BOK
Hg19::chr2:242509651..242509655,+p@chr2:242509651..242509655
+


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
cell layer8.97e-34309
epithelium1.98e-33306
anatomical conduit2.12e-31240
anatomical cluster3.09e-30373
tube6.05e-29192
multi-tissue structure1.95e-22342
multi-cellular organism3.95e-20656
epithelial tube1.60e-18117
anatomical system8.06e-18624
anatomical group1.79e-17625
organ part1.68e-15218
vasculature2.30e-1578
vascular system2.30e-1578
organism subdivision1.61e-14264
unilaminar epithelium2.92e-14148
vessel1.81e-1368
embryo4.29e-13592
developing anatomical structure8.72e-13581
trunk1.25e-12199
structure with developmental contribution from neural crest3.68e-12132
ecto-epithelium6.59e-12104
embryonic structure1.11e-11564
neural plate1.41e-1182
presumptive neural plate1.41e-1182
trunk mesenchyme2.65e-11122
splanchnic layer of lateral plate mesoderm7.82e-1183
neural tube8.83e-1156
neural rod8.83e-1156
future spinal cord8.83e-1156
neural keel8.83e-1156
epithelial tube open at both ends8.97e-1159
blood vessel8.97e-1159
blood vasculature8.97e-1159
vascular cord8.97e-1159
germ layer9.93e-11560
germ layer / neural crest9.93e-11560
embryonic tissue9.93e-11560
presumptive structure9.93e-11560
germ layer / neural crest derived structure9.93e-11560
epiblast (generic)9.93e-11560
organ system subdivision1.21e-10223
regional part of nervous system3.03e-1053
regional part of brain3.03e-1053
mesenchyme3.54e-10160
entire embryonic mesenchyme3.54e-10160
neurectoderm4.55e-1086
simple squamous epithelium6.04e-1022
ectoderm-derived structure1.88e-09171
ectoderm1.88e-09171
presumptive ectoderm1.88e-09171
brain3.32e-0968
future brain3.32e-0968
squamous epithelium3.95e-0925
blood vessel endothelium5.30e-0918
endothelium5.30e-0918
cardiovascular system endothelium5.30e-0918
central nervous system6.95e-0981
subdivision of trunk7.75e-09112
pre-chordal neural plate2.85e-0861
brain grey matter3.73e-0834
gray matter3.73e-0834
nervous system5.65e-0889
telencephalon6.21e-0834
cardiovascular system9.36e-08109
epithelial vesicle1.60e-0778
regional part of telencephalon2.58e-0732
parenchyma2.84e-0715
artery3.49e-0742
arterial blood vessel3.49e-0742
arterial system3.49e-0742
circulatory system3.55e-07112
regional part of forebrain4.13e-0741
forebrain4.13e-0741
anterior neural tube4.13e-0741
future forebrain4.13e-0741
nephron epithelium5.37e-0715
renal tubule5.37e-0715
nephron tubule5.37e-0715
nephron5.37e-0715
uriniferous tubule5.37e-0715
nephrogenic mesenchyme5.37e-0715
cerebral hemisphere5.80e-0732


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)
MA0003.11.54338
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
MA0057.10.333427
MA0058.11.70328
MA0059.10.714521
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
MA0073.10.0834661
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
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.12.30945
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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

No analysis results for this cluster

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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