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

Latest revision as of 11:43, 17 September 2013


Full id: C1373_occipital_hippocampus_caudate_amygdala_medial_thalamus_parietal



Phase1 CAGE Peaks

Hg19::chr12:93800048..93800052,-p@chr12:93800048..93800052
-
Hg19::chr14:90872497..90872510,+p4@CALM1
Hg19::chr3:178865887..178865938,+p2@PIK3CA
Hg19::chr7:44259054..44259069,-p5@CAMK2B
Hg19::chrX:102564877..102564913,-p@chrX:102564877..102564913
-
Hg19::chrX:13805158..13805159,-p@chrX:13805158..13805159
-


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
2.74916378593662e-050.00193357852944209287ErbB signaling pathway (KEGG):04012
0.0001142228966164090.004496981067783682177Calcium signaling pathway (KEGG):04020
2.20729154564608e-050.00193357852944209278Phosphatidylinositol signaling system (KEGG):04070
4.73033289875392e-050.002495250604092692114Oocyte meiosis (KEGG):04114
1.77542685881244e-050.00193357852944209270Long-term potentiation (KEGG):04720
8.59991458038641e-082.7218729646923e-053127Neurotrophin signaling pathway (KEGG):04722
0.00054784231840490.01733920937751512388Olfactory transduction (KEGG):04740
6.93847325306698e-050.003378502745531842138Insulin signaling pathway (KEGG):04910
3.70989802916306e-050.002134877684054742101GnRH signaling pathway (KEGG):04912
3.70989802916306e-050.002134877684054742101Melanogenesis (KEGG):04916
1.98549864581673e-050.00193357852944209274Gastric acid secretion (KEGG):04971
0.0001207720034001940.004496981067783682182Tuberculosis (KEGG):05152
1.12679195761913e-087.13259309172909e-06365Glioma (KEGG):05214
2.74916378593662e-050.00193357852944209287MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
8.75676438203826e-050.003695354569220152155Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
0.001365641663999860.0360187988879963113Keap1-Nrf2 Pathway (Wikipathways):WP3
5.73832218607515e-060.000908089485946393240G13 Signaling Pathway (Wikipathways):WP524
8.09096463176418e-050.003658271865647662149Calcium Regulation in the Cardiac Cell (Wikipathways):WP536
0.0009480760176695820.02727873269022022511Signaling in Immune system (Reactome):REACT_6900
0.0001764801478935890.005879575453507472220Signalling by NGF (Reactome):REACT_11061
0.0007891374383245530.02378685706949722466Hemostasis (Reactome):REACT_604
0.0001415095620414950.004976419598459242197Synaptic Transmission (Reactome):REACT_13685
0.001155623923540870.0318047801565813111Metabolism of nitric oxide (Reactome):REACT_12508
3.20096624129033e-060.00067540387691226230{CALM1,30} (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:0046934phosphatidylinositol-4,5-bisphosphate 3-kinase activity0.0111097667590962
GO:0035004phosphoinositide 3-kinase activity0.0111097667590962
GO:00163031-phosphatidylinositol-3-kinase activity0.0111097667590962
GO:0005942phosphoinositide 3-kinase complex0.0111097667590962
GO:0004683calmodulin-dependent protein kinase activity0.0111097667590962
GO:0046854phosphoinositide phosphorylation0.0111097667590962
GO:0046834lipid phosphorylation0.0111097667590962
GO:0016310phosphorylation0.0111097667590962
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0111097667590962
GO:0001727lipid kinase activity0.0113184485970462
GO:0006793phosphorus metabolic process0.0113184485970462
GO:0006796phosphate metabolic process0.0113184485970462
GO:0016301kinase activity0.0113184485970462
GO:0030258lipid modification0.0128916966733399
GO:0016772transferase activity, transferring phosphorus-containing groups0.0130998092213604
GO:0004428inositol or phosphatidylinositol kinase activity0.0143142684290914
GO:0030384phosphoinositide metabolic process0.0163266350470889
GO:0006650glycerophospholipid metabolic process0.0194612206254854
GO:0043412biopolymer modification0.0213143187492112
GO:0048015phosphoinositide-mediated signaling0.0223615365053458
GO:0005516calmodulin binding0.0232736708268528
GO:0016740transferase activity0.0247950620212862
GO:0044445cytosolic part0.0286138871299826
GO:0006644phospholipid metabolic process0.0310183030141691
GO:0019932second-messenger-mediated signaling0.0361926776864339
GO:0006643membrane lipid metabolic process0.0361926776864339



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
neural tube1.10e-3656
neural rod1.10e-3656
future spinal cord1.10e-3656
neural keel1.10e-3656
adult organism1.35e-36114
regional part of nervous system1.62e-3453
regional part of brain1.62e-3453
central nervous system8.45e-3281
nervous system9.30e-3289
regional part of forebrain5.67e-3141
forebrain5.67e-3141
anterior neural tube5.67e-3141
future forebrain5.67e-3141
brain2.73e-2768
future brain2.73e-2768
neurectoderm1.41e-2686
neural plate2.89e-2682
presumptive neural plate2.89e-2682
brain grey matter3.06e-2634
gray matter3.06e-2634
telencephalon4.62e-2634
cerebral hemisphere7.23e-2532
regional part of telencephalon8.92e-2532
structure with developmental contribution from neural crest9.50e-22132
ecto-epithelium1.24e-21104
ectoderm-derived structure1.39e-20171
ectoderm1.39e-20171
presumptive ectoderm1.39e-20171
pre-chordal neural plate7.20e-2061
cerebral cortex8.69e-2025
pallium8.69e-2025
regional part of cerebral cortex1.36e-1822
neocortex5.02e-1720
organ system subdivision1.64e-13223
basal ganglion5.51e-089
nuclear complex of neuraxis5.51e-089
aggregate regional part of brain5.51e-089
collection of basal ganglia5.51e-089
cerebral subcortex5.51e-089
neural nucleus7.07e-089
nucleus of brain7.07e-089
posterior neural tube2.98e-0715
chordal neural plate2.98e-0715
tube5.62e-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)
MA0003.10.0799681
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.11.41501
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
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
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
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
MA0114.10.845337
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
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.813808
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

No analysis results for this cluster

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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