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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:31, 17 September 2013


Full id: C795_occipital_postcentral_Whole_temporal_paracentral_insula_parietal



Phase1 CAGE Peaks

Hg19::chr11:124609823..124609869,+p1@NRGN
Hg19::chr11:124615457..124615462,+p@chr11:124615457..124615462
+
Hg19::chr11:124615557..124615575,+p@chr11:124615557..124615575
+
Hg19::chr11:124616356..124616367,-p6@ENST00000531241
Hg19::chr11:124616378..124616428,-p2@ENST00000531241
Hg19::chr11:124616466..124616477,-p8@ENST00000531241
Hg19::chr11:124616487..124616565,-p1@ENST00000531241
Hg19::chr11:124616678..124616697,-p10@ENST00000531241
Hg19::chr11:124616843..124616873,-p@chr11:124616843..124616873
-
Hg19::chr16:2564254..2564305,+p@chr16:2564254..2564305
+


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:0005516calmodulin binding0.0415047686329919



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
classical monocyte5.10e-0842
CD14-positive, CD16-negative classical monocyte5.10e-0842
monopoietic cell9.72e-0859
monocyte9.72e-0859
monoblast9.72e-0859
promonocyte9.72e-0859
macrophage dendritic cell progenitor2.69e-0761
defensive cell2.74e-0748
phagocyte2.74e-0748
Uber Anatomy
Ontology termp-valuen
telencephalon1.17e-2934
cerebral hemisphere1.22e-2932
regional part of forebrain2.59e-2741
forebrain2.59e-2741
anterior neural tube2.59e-2741
future forebrain2.59e-2741
brain grey matter5.05e-2734
gray matter5.05e-2734
regional part of telencephalon5.37e-2732
regional part of cerebral cortex8.92e-2422
regional part of nervous system1.57e-2353
regional part of brain1.57e-2353
adult organism1.77e-23114
neural tube2.60e-2356
neural rod2.60e-2356
future spinal cord2.60e-2356
neural keel2.60e-2356
neocortex4.58e-2120
cerebral cortex2.87e-2025
pallium2.87e-2025
brain5.30e-2068
future brain5.30e-2068
central nervous system1.25e-1981
nervous system1.62e-1889
pre-chordal neural plate1.07e-1761
neurectoderm2.84e-1686
neural plate1.70e-1582
presumptive neural plate1.70e-1582
blood2.07e-1415
haemolymphatic fluid2.07e-1415
organism substance2.07e-1415
hematopoietic system1.06e-1198
blood island1.06e-1198
basal ganglion3.90e-119
nuclear complex of neuraxis3.90e-119
aggregate regional part of brain3.90e-119
collection of basal ganglia3.90e-119
cerebral subcortex3.90e-119
ecto-epithelium8.38e-11104
gyrus8.50e-116
hemolymphoid system2.23e-10108
limbic system6.67e-095
temporal lobe8.15e-096
telencephalic nucleus2.76e-087
neural nucleus3.58e-089
nucleus of brain3.58e-089
structure with developmental contribution from neural crest4.06e-08132
germ layer6.45e-08560
germ layer / neural crest6.45e-08560
embryonic tissue6.45e-08560
presumptive structure6.45e-08560
germ layer / neural crest derived structure6.45e-08560
epiblast (generic)6.45e-08560
developing anatomical structure8.46e-08581
embryonic structure1.15e-07564
corpus striatum1.55e-074
striatum1.55e-074
ventral part of telencephalon1.55e-074
future corpus striatum1.55e-074
ectoderm-derived structure3.30e-07171
ectoderm3.30e-07171
presumptive ectoderm3.30e-07171
embryo3.92e-07592
tube5.33e-07192


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)
MA0003.11.34002
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.284587
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.11.99525
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.174262
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.12.52017
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.11.70366
MA0089.10
MA0090.12.35126
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.11.1801
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.945459
MA0146.10.4029
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.21.21406
MA0035.20.437071
MA0039.22.12191
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.20.0329985
MA0065.20.615279
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.10.545933
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.64451
MA0160.10.417847
MA0161.10
MA0162.12.45203
MA0163.11.66479
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.21.38779
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
CTBP2#1488850.17360027146251.81009809364417e-132.75575560936011e-11
CTCF#1066463.216153823845020.004429095326154860.0209696852426804
EGR1#195873.49172536636710.0008771692339228240.00654221792627764
ELF1#199772.980668571165280.002378202870469130.0134723980033047
JUND#372764.196798365122620.001065203456546050.00752392694428604
RAD21#588555.177516947728160.001393960115380.00907177221399378
SMC3#912669.02695970695971.43128844366218e-050.00034229982543539
SP1#666763.419028826884540.003207339839120720.0168217428543127
YY1#752862.946702449912310.006987247873951880.029538197964285
ZNF143#770256.750438276113950.0004088269908565020.00389788954702047



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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