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{{Coexpression_clusters
{
|full_id=C1570_Hepatocyte_liver_left_heart_skeletal_tongue_diaphragm
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Latest revision as of 11:47, 17 September 2013


Full id: C1570_Hepatocyte_liver_left_heart_skeletal_tongue_diaphragm



Phase1 CAGE Peaks

Hg19::chr10:13342051..13342071,-p1@PHYH
Hg19::chr12:121163602..121163682,+p1@ACADS
Hg19::chr16:75150620..75150634,-p3@LDHD
Hg19::chr16:75150636..75150660,-p2@LDHD
Hg19::chr16:75150665..75150699,-p1@LDHD


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

GO IDGO nameFDR corrected p-value
GO:0050660FAD binding0.00131077638607208
GO:0016898oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor0.00131077638607208
GO:0004085butyryl-CoA dehydrogenase activity0.00131077638607208
GO:0048244phytanoyl-CoA dioxygenase activity0.00131077638607208
GO:0004458D-lactate dehydrogenase (cytochrome) activity0.00131077638607208
GO:0016491oxidoreductase activity0.00131077638607208
GO:0050662coenzyme binding0.00252025744769239
GO:0048037cofactor binding0.00480635273047931
GO:0004457lactate dehydrogenase activity0.00784192485112926
GO:0051384response to glucocorticoid stimulus0.00784192485112926
GO:0042594response to starvation0.00784192485112926
GO:0031960response to corticosteroid stimulus0.00784192485112926
GO:0006635fatty acid beta-oxidation0.0103388688314331
GO:0000062acyl-CoA binding0.0103388688314331
GO:0031418L-ascorbic acid binding0.0106139469702964
GO:0006629lipid metabolic process0.0110433382966838
GO:0044444cytoplasmic part0.0110433382966838
GO:0005739mitochondrion0.0110433382966838
GO:0019395fatty acid oxidation0.0110433382966838
GO:0005504fatty acid binding0.0112140400163391
GO:0003995acyl-CoA dehydrogenase activity0.0113684032972744
GO:0048545response to steroid hormone stimulus0.0121655770979493
GO:0031667response to nutrient levels0.0188574475442301
GO:0009991response to extracellular stimulus0.0198753797249594
GO:0009725response to hormone stimulus0.0219648576348286
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0230605676661953
GO:0042579microbody0.0257863391494672
GO:0005777peroxisome0.0257863391494672
GO:0005737cytoplasm0.0301974184667569
GO:0050954sensory perception of mechanical stimulus0.0307149913056266
GO:0007605sensory perception of sound0.0307149913056266
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0371577689188984
GO:0031980mitochondrial lumen0.0387665654934522
GO:0005759mitochondrial matrix0.0387665654934522
GO:0006631fatty acid metabolic process0.0388668101039779
GO:0043231intracellular membrane-bound organelle0.0388668101039779
GO:0043227membrane-bound organelle0.0388668101039779
GO:0007601visual perception0.0411351438598265
GO:0050953sensory perception of light stimulus0.0411351438598265
GO:0030554adenyl nucleotide binding0.0429608724425231
GO:0019842vitamin binding0.0429608724425231
GO:0009055electron carrier activity0.0432971760442599
GO:0032787monocarboxylic acid metabolic process0.0479254241381839



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
fat cell3.90e-0815
Uber Anatomy
Ontology termp-valuen
adult organism3.33e-33114
neural tube2.64e-1356
neural rod2.64e-1356
future spinal cord2.64e-1356
neural keel2.64e-1356
regional part of nervous system2.47e-1253
regional part of brain2.47e-1253
organ system subdivision1.34e-11223
central nervous system6.44e-1181
brain1.12e-1068
future brain1.12e-1068
neural plate4.14e-1082
presumptive neural plate4.14e-1082
nervous system4.49e-1089
regional part of forebrain6.09e-1041
forebrain6.09e-1041
anterior neural tube6.09e-1041
future forebrain6.09e-1041
telencephalon5.03e-0934
brain grey matter5.18e-0934
gray matter5.18e-0934
multi-cellular organism8.21e-09656
organ1.02e-08503
neurectoderm1.39e-0886
cerebral hemisphere3.46e-0832
regional part of telencephalon3.77e-0832
multi-tissue structure5.51e-08342
anatomical cluster2.25e-07373
structure with developmental contribution from neural crest5.48e-07132
ecto-epithelium6.19e-07104
regional part of cerebral cortex8.47e-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)
MA0003.11.80249
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.13.37159
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
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
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.12.39477
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.12.57792
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.13.51336
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.24205
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.146371
MA0102.21.66336
MA0258.11.63655
MA0259.10.395396
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
FOSL2#2355310.1581203627370.001881990703415430.0110890396092527
HEY1#2346254.040111043105710.0009288852205177990.00673459517845598
MAX#414945.16204440720570.002526309009485180.0139926382393733
RFX5#599337.228746496317060.00502918278958660.0234619565534299
SIN3A#2594255.408884726815140.0002159522671657270.00247681076548664
SP1#666744.558705102512720.00407573565781680.01947324929625
TAF1#687253.343046285745290.002394600090870310.0135088661421922
TAF7#687936.859841642954350.005843286407019040.0262390140623726
TBP#690853.706770687096390.001428755106721120.00917585503571807



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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