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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.060502893194481

Latest revision as of 11:43, 17 September 2013


Full id: C1381_corpus_thyroid_cerebellum_pineal_thalamus_pituitary_substantia



Phase1 CAGE Peaks

Hg19::chr13:41495851..41495883,-p1@SUGT1P3
Hg19::chr19:40502938..40502987,+p1@ZNF546
Hg19::chr22:38577782..38577858,-p1@PLA2G6
Hg19::chr2:203776982..203777014,+p1@ALS2CR8
Hg19::chr2:232646379..232646423,+p3@COPS7B
Hg19::chr4:74124877..74124918,+p1@ENST00000502790


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>

Cell Type
Ontology termp-valuen
nucleate cell1.45e-1155
lymphoid lineage restricted progenitor cell2.91e-1152
lymphocyte2.99e-1153
common lymphoid progenitor2.99e-1153
mature alpha-beta T cell2.95e-0818
alpha-beta T cell2.95e-0818
immature T cell2.95e-0818
mature T cell2.95e-0818
immature alpha-beta T cell2.95e-0818
T cell1.26e-0725
pro-T cell1.26e-0725
Uber Anatomy
Ontology termp-valuen
adult organism6.66e-47114
neural tube6.56e-3056
neural rod6.56e-3056
future spinal cord6.56e-3056
neural keel6.56e-3056
regional part of nervous system4.46e-2853
regional part of brain4.46e-2853
central nervous system2.20e-2581
nervous system2.99e-2589
brain6.75e-2568
future brain6.75e-2568
regional part of forebrain1.46e-2341
forebrain1.46e-2341
anterior neural tube1.46e-2341
future forebrain1.46e-2341
neurectoderm9.36e-2186
neural plate8.22e-2082
presumptive neural plate8.22e-2082
telencephalon4.03e-1934
brain grey matter4.41e-1934
gray matter4.41e-1934
regional part of telencephalon7.73e-1832
cerebral hemisphere9.35e-1832
pre-chordal neural plate4.27e-1561
regional part of cerebral cortex4.10e-1422
cerebral cortex1.90e-1325
pallium1.90e-1325
neocortex6.31e-1320
ectoderm-derived structure1.30e-12171
ectoderm1.30e-12171
presumptive ectoderm1.30e-12171
ecto-epithelium1.51e-12104
organ system subdivision6.47e-09223
structure with developmental contribution from neural crest2.44e-08132
posterior neural tube1.49e-0715
chordal neural plate1.49e-0715
neural nucleus3.41e-079
nucleus of brain3.41e-079
basal ganglion4.06e-079
nuclear complex of neuraxis4.06e-079
aggregate regional part of brain4.06e-079
collection of basal ganglia4.06e-079
cerebral subcortex4.06e-079


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)
MA0003.10.321379
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.11.45353
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.11.15845
MA0060.10.737586
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.12.86388
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.107156
MA0146.11.05598
MA0147.10.87383
MA0148.10.584698
MA0149.12.52795
MA0062.21.22729
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.20.255126
MA0137.21.87543
MA0104.21.35181
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0318308
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
ATF3#467311.23158726300440.001593459971184230.0100403840682057
E2F1#186964.907389214879327.15746523583771e-050.00112679908315595
ELF1#199764.258097958807540.0001677224776288830.00205210494858047
ELK4#200538.117840829234010.004056113134185760.0194079076199765
FOXA1#316935.540709874692730.01192178777860280.0433787267466641
GABPB1#255355.889736530151810.0003000175973670210.00309834251472504
HEY1#2346264.040111043105710.0002298968555807510.00253085250342553
MAX#414944.301703672671410.006644923910676370.028296061661385
NFKB1#479054.57338618682820.00102196259371130.00724397660680155
NRF1#489948.140186298473940.0005892175548383380.00493482696148846
PAX5#507944.446377020785220.005874733519240790.0263609578524592
POLR2A#543062.147453176558070.01019570676818780.0380106168045537
POU2F2#545246.070749371828350.001815326209524520.0108935218338618
SIX5#147912514.23892946288253.91539088341565e-060.000127508421725303
SREBF2#6721172.82387706855790.01365361575289130.0481697792661626
SRF#672249.19811884144520.0003672404582485860.00365766032987069
TAF1#687263.343046285745290.0007162474284635620.0057290468852957
TBP#690863.706770687096390.000385416472907960.00377674151004264
TCF7L2#693435.385088281568670.01290488779931040.046404544032233
YY1#752854.092642291544880.001743365462849530.0107248245022408
ZBTB33#10009210.55490834332710.01374250737140590.0483853193325779
ZNF143#7702511.25073046018991.25426047727876e-050.000309239164274119
ZNF263#1012745.481227758007120.002675609380607230.0147445107693773



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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