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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0100683094419722

Latest revision as of 11:45, 17 September 2013


Full id: C1476_Neurons_iPS_occipital_temporal_parietal_duodenum_spinal



Phase1 CAGE Peaks

Hg19::chr1:32799593..32799616,-p2@BX648622
Hg19::chr1:32799709..32799739,-p1@BX648622
Hg19::chr1:32799803..32799823,-p@chr1:32799803..32799823
-
Hg19::chr1:32799908..32799938,-p@chr1:32799908..32799938
-
Hg19::chr1:32800048..32800094,-p@chr1:32800048..32800094
-
Hg19::chr1:32800303..32800316,-p@chr1:32800303..32800316
-


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
endothelial cell8.94e-0736
Uber Anatomy
Ontology termp-valuen
central nervous system4.30e-1781
nervous system1.84e-1689
anatomical cluster1.23e-13373
neurectoderm7.27e-1386
neural tube1.76e-1256
neural rod1.76e-1256
future spinal cord1.76e-1256
neural keel1.76e-1256
neural plate4.95e-1282
presumptive neural plate4.95e-1282
tube7.40e-12192
epithelium1.29e-11306
cell layer1.45e-11309
brain1.53e-1168
future brain1.53e-1168
regional part of nervous system5.10e-1153
regional part of brain5.10e-1153
brain grey matter6.98e-1034
gray matter6.98e-1034
telencephalon1.31e-0934
anatomical conduit2.47e-09240
pre-chordal neural plate3.29e-0961
regional part of telencephalon4.60e-0932
cerebral hemisphere1.18e-0832
embryo1.78e-08592
organ system subdivision4.00e-08223
regional part of forebrain5.01e-0841
forebrain5.01e-0841
anterior neural tube5.01e-0841
future forebrain5.01e-0841
developing anatomical structure9.57e-08581
ecto-epithelium1.05e-07104
cerebral cortex2.20e-0725
pallium2.20e-0725
structure with developmental contribution from neural crest2.92e-07132
germ layer4.37e-07560
germ layer / neural crest4.37e-07560
embryonic tissue4.37e-07560
presumptive structure4.37e-07560
germ layer / neural crest derived structure4.37e-07560
epiblast (generic)4.37e-07560
multi-cellular organism5.20e-07656
embryonic structure5.65e-07564


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.15.06808
MA0031.13.34657
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.12.36274
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.12.74425
MA0101.10.397846
MA0103.10.993014
MA0105.11.34409
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
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
MA0144.10.299851
MA0145.10.107156
MA0146.10.441872
MA0147.10.327615
MA0148.11.42897
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.200862
MA0138.23.01409
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.21.66123
MA0112.20.101413
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.11.89858
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.10486
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
POLR2A#543062.147453176558070.01019570676818780.0380459275104604



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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