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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.169980192088818,-0

Latest revision as of 12:06, 17 September 2013


Full id: C2485_pineal_cerebellum_pituitary_parietal_occipital_CD4_duodenum



Phase1 CAGE Peaks

Hg19::chr19:36980429..36980448,-p1@ZNF566
Hg19::chr19:38270215..38270251,-p1@ZNF573
Hg19::chr19:40562072..40562143,-p1@ZNF780B
Hg19::chr5:179285785..179285846,-p1@C5orf45


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

p.valueFDRnGenesnPathwayName
1.00202116011964e-050.006342793943557343390{ASH2L,391} (Static Module):NA



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:0006355regulation of transcription, DNA-dependent0.00519923459098235
GO:0006351transcription, DNA-dependent0.00519923459098235
GO:0032774RNA biosynthetic process0.00519923459098235
GO:0003677DNA binding0.00519923459098235
GO:0045449regulation of transcription0.00519923459098235
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00519923459098235
GO:0006350transcription0.00519923459098235
GO:0010468regulation of gene expression0.00519923459098235
GO:0031323regulation of cellular metabolic process0.00519923459098235
GO:0019222regulation of metabolic process0.00519923459098235
GO:0016070RNA metabolic process0.00519923459098235
GO:0008270zinc ion binding0.00519923459098235
GO:0046914transition metal ion binding0.00784871922371737
GO:0010467gene expression0.0100445935106716
GO:0050794regulation of cellular process0.0107243941177873
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0108351071276006
GO:0005634nucleus0.011147418527857
GO:0050789regulation of biological process0.011147418527857
GO:0003676nucleic acid binding0.0118316479005403
GO:0043169cation binding0.0118867181787075
GO:0065007biological regulation0.0125886689188592
GO:0046872metal ion binding0.0126208906693392
GO:0043167ion binding0.0126967359708667
GO:0043283biopolymer metabolic process0.0180817341916611
GO:0043231intracellular membrane-bound organelle0.0229336055866812
GO:0043227membrane-bound organelle0.0229336055866812
GO:0043229intracellular organelle0.0386616181848527
GO:0043226organelle0.0386616181848527
GO:0043170macromolecule metabolic process0.0413773157609536



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 organism2.24e-37114
neural tube6.04e-2756
neural rod6.04e-2756
future spinal cord6.04e-2756
neural keel6.04e-2756
central nervous system1.19e-2681
nervous system1.99e-2689
regional part of nervous system1.25e-2553
regional part of brain1.25e-2553
brain6.09e-2368
future brain6.09e-2368
regional part of forebrain3.20e-2241
forebrain3.20e-2241
anterior neural tube3.20e-2241
future forebrain3.20e-2241
neurectoderm2.60e-2086
neural plate1.64e-1982
presumptive neural plate1.64e-1982
telencephalon1.87e-1834
brain grey matter2.54e-1834
gray matter2.54e-1834
regional part of telencephalon1.94e-1732
cerebral hemisphere2.33e-1732
pre-chordal neural plate8.87e-1561
regional part of cerebral cortex4.74e-1422
cerebral cortex1.17e-1325
pallium1.17e-1325
organ system subdivision4.46e-13223
neocortex7.37e-1320
ectoderm-derived structure8.55e-13171
ectoderm8.55e-13171
presumptive ectoderm8.55e-13171
ecto-epithelium3.64e-12104
structure with developmental contribution from neural crest3.79e-11132


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)
MA0003.10.443649
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.25938
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
E2F6#187645.017155731697390.00157802193473060.00996957430532508
GABPB1#255335.300762877136630.01012678824234270.0378604488005023
HEY1#2346244.040111043105710.00375304636917980.0186082610022204
NR2C2#7182216.30730545262040.005411825344648220.0245538740679315
SETDB1#9869220.16001308900520.00356908685407640.018086848559022
SIX5#147912312.81503651659420.0007664471136930380.006016307411273
TAF1#687243.343046285745290.008005664898701650.0322272446945537
TAF7#687938.574802053692940.00250055433515240.0140330679317024
TBP#690843.706770687096390.005296377814784350.0244258766492212
ZNF143#7702413.50087655222793.00867915035614e-050.000621117694769806
ZNF263#1012736.166381227758010.006539814347975980.0279750837881738



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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