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Coexpression cluster:C4090

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Full id: C4090_salivary_Hepatocyte_liver_parotid_submaxillary_tongue_lung



Phase1 CAGE Peaks

Hg19::chr22:25507144..25507210,+p@chr22:25507144..25507210
+
Hg19::chr22:25507901..25507915,+p@chr22:25507901..25507915
+
Hg19::chr22:25507920..25507932,+p@chr22:25507920..25507932
+


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.24e-53114
anatomical cluster3.92e-22373
organ system subdivision1.92e-21223
regional part of nervous system4.96e-2153
regional part of brain4.96e-2153
anatomical conduit8.74e-21240
neural tube9.68e-2156
neural rod9.68e-2156
future spinal cord9.68e-2156
neural keel9.68e-2156
regional part of forebrain1.02e-1941
forebrain1.02e-1941
anterior neural tube1.02e-1941
future forebrain1.02e-1941
neural plate2.49e-1982
presumptive neural plate2.49e-1982
pre-chordal neural plate7.57e-1861
neurectoderm8.62e-1886
brain1.04e-1768
future brain1.04e-1768
central nervous system1.04e-1681
brain grey matter3.45e-1534
gray matter3.45e-1534
multi-tissue structure4.37e-15342
ectoderm-derived structure4.51e-15171
ectoderm4.51e-15171
presumptive ectoderm4.51e-15171
ecto-epithelium6.23e-15104
cerebral hemisphere9.19e-1532
telencephalon9.48e-1534
nervous system8.24e-1489
regional part of telencephalon2.07e-1332
tube5.30e-13192
regional part of cerebral cortex6.17e-1322
organ6.98e-13503
neocortex7.43e-1320
structure with developmental contribution from neural crest6.44e-12132
anatomical system2.91e-11624
anatomical group3.50e-11625
multi-cellular organism5.03e-11656
cerebral cortex7.53e-1125
pallium7.53e-1125
epithelium2.43e-10306
cell layer5.04e-10309
subdivision of digestive tract8.56e-10118
embryo9.16e-10592
developing anatomical structure1.51e-09581
exocrine gland2.80e-0931
exocrine system2.80e-0931
germ layer3.58e-09560
germ layer / neural crest3.58e-09560
embryonic tissue3.58e-09560
presumptive structure3.58e-09560
germ layer / neural crest derived structure3.58e-09560
epiblast (generic)3.58e-09560
gland3.88e-0959
embryonic structure7.18e-09564
saliva-secreting gland8.54e-096
gland of oral region8.54e-096
gland of foregut8.54e-096
oral gland8.54e-096
oral cavity8.54e-096
digestive system1.48e-08145
digestive tract1.48e-08145
primitive gut1.48e-08145
foregut1.54e-0887
endoderm-derived structure1.91e-08160
endoderm1.91e-08160
presumptive endoderm1.91e-08160
organ part2.13e-08218
brainstem2.05e-076
diencephalon8.75e-077
future diencephalon8.75e-077


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)
MA0003.10.0471418
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
MA0031.12.60497
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
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
MA0073.113.9778
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
MA0093.10.642957
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
MA0113.12.29491
MA0114.11.35563
MA0115.11.57693
MA0116.13.4624
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.23.66129
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
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
CTCF#1066435.360256373075030.0064925092527670.0279986445556914
FOXA1#3169311.08141974938550.000734755275698670.00582179699861113
FOXA2#3170324.63046375266526.68983856509345e-050.00107357106622587
USF1#739136.361499277207960.00388404057290560.0190667597364836



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.