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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0362496447385107,0

Latest revision as of 12:13, 17 September 2013


Full id: C2826_Mast_medial_frontal_occipital_parietal_brain_olfactory



Phase1 CAGE Peaks

Hg19::chr5:67586544..67586558,+p7@PIK3R1
Hg19::chr5:67588391..67588411,+p13@PIK3R1
Hg19::chr5:67588419..67588430,+p29@PIK3R1
Hg19::chr6:147453079..147453129,-p1@ENST00000431143
p1@uc003qlv.2


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
0.003047712464093040.049893154907868187ErbB signaling pathway (KEGG):04012
0.002732431864359280.049893154907868178Phosphatidylinositol signaling system (KEGG):04070
0.001821621242906190.049893154907868152mTOR signaling pathway (KEGG):04150
0.003012681286344850.049893154907868186Apoptosis (KEGG):04210
0.002662369508862890.049893154907868176VEGF signaling pathway (KEGG):04370
0.003573180130315980.0498931549078681102Toll-like receptor signaling pathway (KEGG):04620
0.003783367196805160.0498931549078681108T cell receptor signaling pathway (KEGG):04660
0.002627338331114690.049893154907868175B cell receptor signaling pathway (KEGG):04662
0.002767463042107480.049893154907868179Fc epsilon RI signaling pathway (KEGG):04664
0.003327961886078610.049893154907868195Fc gamma R-mediated phagocytosis (KEGG):04666
0.003047712464093040.049893154907868187Progesterone-mediated oocyte maturation (KEGG):04914
0.00168149653191340.049893154907868148Type II diabetes mellitus (KEGG):04930
0.001471309465424230.049893154907868142Aldosterone-regulated sodium reabsorption (KEGG):04960
0.001541371820920620.049893154907868144Carbohydrate digestion and absorption (KEGG):04973
0.002487213620121910.049893154907868171Bacterial invasion of epithelial cells (KEGG):05100
0.003643242485812370.0498931549078681104Chagas disease (American trypanosomiasis) (KEGG):05142
0.003713304841308770.0498931549078681106Amoebiasis (KEGG):05146
0.002171933020388140.049893154907868162Colorectal cancer (KEGG):05210
0.002452182442373710.049893154907868170Renal cell carcinoma (KEGG):05211
0.002452182442373710.049893154907868170Pancreatic cancer (KEGG):05212
0.001821621242906190.049893154907868152Endometrial cancer (KEGG):05213
0.002277026553632730.049893154907868165Glioma (KEGG):05214
0.003117774819589430.049893154907868189Prostate cancer (KEGG):05215
0.002487213620121910.049893154907868171Melanoma (KEGG):05218
0.00255727597561830.049893154907868173Chronic myeloid leukemia (KEGG):05220
0.002031808309395360.049893154907868158Acute myeloid leukemia (KEGG):05221
0.002977650108596650.049893154907868185Small cell lung cancer (KEGG):05222
0.001891683598402580.049893154907868154Non-small cell lung cancer (KEGG):05223
0.002417151264625520.049893154907868169IL-5 Signaling Pathway (Wikipathways):WP127
0.00255727597561830.049893154907868173AMPK signaling (Wikipathways):WP1403
0.003047712464093040.049893154907868187MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
0.001541371820920620.049893154907868144IL-7 Signaling Pathway (Wikipathways):WP205
0.0008407482659567010.049893154907868124IL-9 Signaling Pathway (Wikipathways):WP22
0.002417151264625520.049893154907868169Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
0.002977650108596650.049893154907868185Apoptosis (Wikipathways):WP254
0.003573180130315980.0498931549078681102IL-3 Signaling Pathway (Wikipathways):WP286
0.002417151264625520.049893154907868169Kit Receptor Signaling Pathway (Wikipathways):WP304
0.003468086597071390.049893154907868199IL-6 Signaling Pathway (Wikipathways):WP364
0.002241995375884540.049893154907868164IL-4 signaling Pathway (Wikipathways):WP395
0.002697400686611080.049893154907868177IL-2 Signaling Pathway (Wikipathways):WP49
0.003012681286344850.049893154907868186Delta-Notch Signaling Pathway (Wikipathways):WP61
0.003573180130315980.0498931549078681102Toll-like receptor signaling pathway (Wikipathways):WP75
0.003783367196805160.0498931549078681108Signaling by Insulin receptor (Reactome):REACT_498
0.001821621242906190.049893154907868152Signaling by EGFR (Reactome):REACT_9417
0.002277026553632730.049893154907868165Signaling by PDGF (Reactome):REACT_16888
0.001576402998668820.049893154907868145Signaling by FGFR (Reactome):REACT_9470
0.001611434176417010.049893154907868146Interactions of the immunoglobulin superfamily (IgSF) member proteins (Reactome):REACT_23853
0.00255727597561830.049893154907868173Notch up reg. targets (Netpath):NetPath_3



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:0035030phosphoinositide 3-kinase complex, class IA0.00167785234899329
GO:0043559insulin binding0.00167785234899329
GO:0043125ErbB-3 class receptor binding0.00209731543624161
GO:0043560insulin receptor substrate binding0.00209731543624161
GO:0048009insulin-like growth factor receptor signaling pathway0.00215723873441994
GO:0017046peptide hormone binding0.00215723873441994
GO:0035014phosphoinositide 3-kinase regulator activity0.00215723873441994
GO:0005159insulin-like growth factor receptor binding0.00230704697986577
GO:0019903protein phosphatase binding0.00272651006711409
GO:0005545phosphatidylinositol binding0.00272651006711409
GO:0005942phosphoinositide 3-kinase complex0.00272651006711409
GO:0019902phosphatase binding0.00272651006711409
GO:0005158insulin receptor binding0.00272651006711409
GO:0046854phosphoinositide phosphorylation0.00272651006711409
GO:0042562hormone binding0.00272651006711409
GO:0046834lipid phosphorylation0.00272651006711409
GO:0008286insulin receptor signaling pathway0.00315831030398737
GO:0030258lipid modification0.00484712900820283
GO:0030384phosphoinositide metabolic process0.00706464146944542
GO:0006650glycerophospholipid metabolic process0.00806967082134867
GO:0032403protein complex binding0.00806967082134867
GO:0019207kinase regulator activity0.00930445393532642
GO:0044445cytosolic part0.0138605194047272
GO:0042277peptide binding0.0138745482705214
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0138745482705214
GO:0006644phospholipid metabolic process0.0138745482705214
GO:0035091phosphoinositide binding0.0155978125776783
GO:0006643membrane lipid metabolic process0.0162991371045062
GO:0007167enzyme linked receptor protein signaling pathway0.0167785234899329
GO:0019899enzyme binding0.0167785234899329
GO:0005125cytokine activity0.0167785234899329
GO:0005543phospholipid binding0.0175125838926175
GO:0005829cytosol0.0285728385313857
GO:0008289lipid binding0.0285728385313857
GO:0044255cellular lipid metabolic process0.036816874400767
GO:0006629lipid metabolic process0.0440902311707681
GO:0005102receptor binding0.0470252131325957



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 organism5.68e-56114
neural tube1.92e-5256
neural rod1.92e-5256
future spinal cord1.92e-5256
neural keel1.92e-5256
regional part of forebrain3.17e-4941
forebrain3.17e-4941
anterior neural tube3.17e-4941
future forebrain3.17e-4941
regional part of nervous system3.93e-4853
regional part of brain3.93e-4853
cerebral hemisphere2.01e-4732
telencephalon4.08e-4734
brain grey matter6.54e-4734
gray matter6.54e-4734
regional part of telencephalon8.57e-4432
regional part of cerebral cortex1.32e-4022
central nervous system6.72e-4081
brain1.26e-3868
future brain1.26e-3868
neocortex5.72e-3720
neural plate2.58e-3582
presumptive neural plate2.58e-3582
cerebral cortex4.70e-3525
pallium4.70e-3525
nervous system1.47e-3489
neurectoderm4.75e-3386
pre-chordal neural plate1.11e-2961
ecto-epithelium1.43e-26104
structure with developmental contribution from neural crest9.45e-24132
organ system subdivision4.99e-22223
ectoderm-derived structure6.50e-22171
ectoderm6.50e-22171
presumptive ectoderm6.50e-22171
basal ganglion1.00e-139
nuclear complex of neuraxis1.00e-139
aggregate regional part of brain1.00e-139
collection of basal ganglia1.00e-139
cerebral subcortex1.00e-139
gyrus2.05e-136
neural nucleus4.32e-139
nucleus of brain4.32e-139
organ part1.78e-12218
occipital lobe4.59e-115
limbic system7.13e-115
parietal lobe7.42e-115
temporal lobe1.24e-106
tube1.67e-10192
anatomical cluster3.33e-10373
telencephalic nucleus4.25e-107
anatomical conduit7.94e-10240
organ9.99e-10503
multi-tissue structure2.84e-09342
corpus striatum8.85e-094
striatum8.85e-094
ventral part of telencephalon8.85e-094
future corpus striatum8.85e-094
brainstem9.08e-086
frontal cortex1.19e-073
caudate-putamen7.10e-073
dorsal striatum7.10e-073


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0055.10.125954
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
MA0088.10.182167
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
MA0145.10.569905
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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