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Coexpression cluster:C2016: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2016_Fibroblast_corpus_Nucleus_Anulus_globus_tridermal_Synoviocyte
|id=C2016
}}

Latest revision as of 11:57, 17 September 2013


Full id: C2016_Fibroblast_corpus_Nucleus_Anulus_globus_tridermal_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr9:113800341..113800373,-p4@LPAR1
Hg19::chr9:113800377..113800400,-p6@LPAR1
Hg19::chr9:113800467..113800520,-p2@LPAR1
Hg19::chr9:113800705..113800781,-p1@LPAR1
Hg19::chr9:113800994..113801032,-p3@LPAR1


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
multi-tissue structure1.12e-22342
multi-cellular organism2.87e-21656
anatomical system6.51e-18624
structure with developmental contribution from neural crest1.24e-17132
anatomical group1.41e-17625
dense mesenchyme tissue1.24e-1573
paraxial mesoderm3.62e-1572
presumptive paraxial mesoderm3.62e-1572
embryonic structure5.22e-15564
multilaminar epithelium5.34e-1583
somite6.62e-1571
presomitic mesoderm6.62e-1571
presumptive segmental plate6.62e-1571
dermomyotome6.62e-1571
trunk paraxial mesoderm6.62e-1571
germ layer6.69e-15560
germ layer / neural crest6.69e-15560
embryonic tissue6.69e-15560
presumptive structure6.69e-15560
germ layer / neural crest derived structure6.69e-15560
epiblast (generic)6.69e-15560
cell layer1.37e-14309
surface structure2.73e-1499
epithelium5.46e-14306
tissue1.17e-13773
developing anatomical structure1.31e-13581
adult organism1.56e-13114
embryo2.15e-13592
muscle tissue7.85e-1364
musculature7.85e-1364
musculature of body7.85e-1364
epithelial vesicle1.22e-1278
neural tube1.36e-1256
neural rod1.36e-1256
future spinal cord1.36e-1256
neural keel1.36e-1256
skeletal muscle tissue1.56e-1262
striated muscle tissue1.56e-1262
myotome1.56e-1262
brain1.65e-1268
future brain1.65e-1268
mesenchyme2.06e-12160
entire embryonic mesenchyme2.06e-12160
organ2.11e-12503
anatomical cluster2.13e-12373
ectoderm-derived structure2.49e-12171
ectoderm2.49e-12171
presumptive ectoderm2.49e-12171
trunk mesenchyme3.28e-11122
nervous system3.40e-1189
regional part of nervous system3.90e-1153
regional part of brain3.90e-1153
organ system subdivision5.50e-11223
organism subdivision6.16e-11264
neural plate7.21e-1182
presumptive neural plate7.21e-1182
central nervous system7.45e-1181
neurectoderm2.19e-1086
ecto-epithelium2.55e-09104
regional part of forebrain3.45e-0941
forebrain3.45e-0941
anterior neural tube3.45e-0941
future forebrain3.45e-0941
telencephalon4.85e-0934
brain grey matter6.54e-0934
gray matter6.54e-0934
anatomical conduit7.43e-09240
regional part of telencephalon4.37e-0832
cerebral hemisphere5.34e-0832
subdivision of skeletal system9.96e-0816
trunk3.01e-07199
integument4.29e-0746
integumental system4.29e-0746
organ part4.52e-07218
organ component layer7.72e-0766
musculoskeletal system7.77e-07167
regional part of cerebral cortex9.28e-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)
MA0003.14.96701
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.11.11255
MA0014.14.38573
MA0017.11.24112
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.13.39561
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.12.59297
MA0119.12.17648
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.11.39943
MA0146.12.90482
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.21.35805
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.14.91907
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.12.27598
MA0163.14.46402
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.26.70786
MA0102.21.66336
MA0258.10.914277
MA0259.11.02361
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
RAD21#588536.21302033727380.007751055068811640.0319007109210127



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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