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Coexpression cluster:C3132: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;3.923,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;2.3269,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.61229,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:09, 22 January 2013


Full id: C3132_Pericytes_Mesenchymal_Skeletal_skeletal_amniotic_Hair_gastric



Phase1 CAGE Peaks

Hg19::chr11:2158507..2158526,-p3@IGF2
Hg19::chr17:48277566..48277608,-p5@COL1A1
Hg19::chr1:168409732..168409736,+p@chr1:168409732..168409736
+


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

GO IDGO nameFDR corrected p-value
GO:0001501skeletal development0.0030134928219141
GO:0005584collagen type I0.0062794040249056
GO:0008147structural constituent of bone0.0062794040249056
GO:0006349genetic imprinting0.0064749681926325
GO:0018445prothoracicotrophic hormone activity0.0064749681926325
GO:0005583fibrillar collagen0.0064749681926325
GO:0005159insulin-like growth factor receptor binding0.0064749681926325
GO:0051591response to cAMP0.0064749681926325
GO:0031960response to corticosteroid stimulus0.00680178652952636
GO:0009612response to mechanical stimulus0.00784740648934456
GO:0048513organ development0.00784740648934456
GO:0042542response to hydrogen peroxide0.00784740648934456
GO:0043434response to peptide hormone stimulus0.00796790119733836
GO:0000302response to reactive oxygen species0.00907963454196166
GO:0008286insulin receptor signaling pathway0.00970930687956354
GO:0005184neuropeptide hormone activity0.00970930687956354
GO:0048545response to steroid hormone stimulus0.00988452957792736
GO:0048731system development0.00988452957792736
GO:0007584response to nutrient0.00988452957792736
GO:0010035response to inorganic substance0.00988452957792736
GO:0005581collagen0.0119441092498285
GO:0048856anatomical structure development0.0119441092498285
GO:0031667response to nutrient levels0.0119441092498285
GO:0010033response to organic substance0.0119441092498285
GO:0040029regulation of gene expression, epigenetic0.0119441092498285
GO:0009991response to extracellular stimulus0.0119441092498285
GO:0009725response to hormone stimulus0.0130795109121471
GO:0007275multicellular organismal development0.0130795109121471
GO:0031214biomineral formation0.0137976083286762
GO:0001503ossification0.0137976083286762
GO:0046849bone remodeling0.014564672669458
GO:0048771tissue remodeling0.0154302476562255
GO:0006979response to oxidative stress0.0166990454661848
GO:0005201extracellular matrix structural constituent0.0166990454661848
GO:0044420extracellular matrix part0.0166990454661848
GO:0050954sensory perception of mechanical stimulus0.0166990454661848
GO:0007605sensory perception of sound0.0166990454661848
GO:0008544epidermis development0.0166990454661848
GO:0006817phosphate transport0.0171539397978626
GO:0007398ectoderm development0.0171539397978626
GO:0009628response to abiotic stimulus0.0184838697208335
GO:0032502developmental process0.0184838697208335
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0226393100151102
GO:0032501multicellular organismal process0.0226393100151102
GO:0005179hormone activity0.0226393100151102
GO:0008083growth factor activity0.0258076074285635
GO:0015698inorganic anion transport0.0259546771181936
GO:0007167enzyme linked receptor protein signaling pathway0.029184688142699
GO:0009888tissue development0.029184688142699
GO:0006820anion transport0.0302808613505519
GO:0005578proteinaceous extracellular matrix0.038638277528768
GO:0009719response to endogenous stimulus0.0475404146506583



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>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure3.01e-24342
organism subdivision1.76e-20264
cell layer2.37e-20309
anatomical cluster2.17e-19373
epithelium5.13e-19306
multi-cellular organism1.36e-18656
mesenchyme1.94e-16160
entire embryonic mesenchyme1.94e-16160
trunk2.16e-15199
anatomical system3.82e-14624
anatomical group8.29e-14625
trunk mesenchyme2.82e-13122
organ part6.20e-12218
embryo2.23e-11592
unilaminar epithelium7.59e-11148
skeletal muscle tissue8.64e-1162
striated muscle tissue8.64e-1162
myotome8.64e-1162
endoderm-derived structure9.07e-11160
endoderm9.07e-11160
presumptive endoderm9.07e-11160
anatomical conduit1.54e-10240
muscle tissue1.74e-1064
musculature1.74e-1064
musculature of body1.74e-1064
developing anatomical structure4.70e-10581
organ5.96e-10503
epithelial vesicle9.53e-1078
multilaminar epithelium3.61e-0983
embryonic structure4.06e-09564
organ system subdivision4.82e-09223
germ layer5.94e-09560
germ layer / neural crest5.94e-09560
embryonic tissue5.94e-09560
presumptive structure5.94e-09560
germ layer / neural crest derived structure5.94e-09560
epiblast (generic)5.94e-09560
dense mesenchyme tissue2.39e-0873
tube4.29e-08192
somite4.60e-0871
presomitic mesoderm4.60e-0871
presumptive segmental plate4.60e-0871
dermomyotome4.60e-0871
trunk paraxial mesoderm4.60e-0871
urinary system structure4.96e-0847
paraxial mesoderm5.76e-0872
presumptive paraxial mesoderm5.76e-0872
renal system6.94e-0848
epithelial tube6.99e-08117
immaterial anatomical entity7.45e-08117
subdivision of trunk1.00e-07112
vasculature of organ1.24e-0711
digestive system1.50e-07145
digestive tract1.50e-07145
primitive gut1.50e-07145
extraembryonic membrane3.89e-0714
membranous layer3.89e-0714
organ component layer4.47e-0766
compound organ6.60e-0768


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.923
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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