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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.175365940065456,

Latest revision as of 12:00, 17 September 2013


Full id: C2155_Alveolar_Mesenchymal_Renal_Hair_Smooth_Fibroblast_Bronchial



Phase1 CAGE Peaks

Hg19::chr11:65625643..65625659,-p1@CFL1
Hg19::chr11:66036082..66036125,+p1@RAB1B
Hg19::chr17:79829190..79829260,-p1@ARHGDIA
Hg19::chr7:5570229..5570234,-p1@ACTB


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:0007264small GTPase mediated signal transduction0.00561280380812922
GO:0006916anti-apoptosis0.00561280380812922
GO:0007266Rho protein signal transduction0.00561280380812922
GO:0043066negative regulation of apoptosis0.00561280380812922
GO:0043069negative regulation of programmed cell death0.00561280380812922
GO:0005856cytoskeleton0.00561280380812922
GO:0035267NuA4 histone acetyltransferase complex0.00898898000577465
GO:0007242intracellular signaling cascade0.00898898000577465
GO:0051674localization of cell0.00898898000577465
GO:0006928cell motility0.00898898000577465
GO:0043189H4/H2A histone acetyltransferase complex0.00898898000577465
GO:0007265Ras protein signal transduction0.00951756176553976
GO:0000123histone acetyltransferase complex0.0134669426856117
GO:0042981regulation of apoptosis0.0134669426856117
GO:0043067regulation of programmed cell death0.0134669426856117
GO:0005094Rho GDP-dissociation inhibitor activity0.0144325718247894
GO:0005737cytoplasm0.0144325718247894
GO:0043232intracellular non-membrane-bound organelle0.0144325718247894
GO:0043228non-membrane-bound organelle0.0144325718247894
GO:0031981nuclear lumen0.0144325718247894
GO:0007162negative regulation of cell adhesion0.017474096358452
GO:0005092GDP-dissociation inhibitor activity0.0179612957941699
GO:0006915apoptosis0.0186480408191993
GO:0012501programmed cell death0.0186480408191993
GO:0016265death0.0190659149538056
GO:0008219cell death0.0190659149538056
GO:0031974membrane-enclosed lumen0.0201966507970214
GO:0043233organelle lumen0.0201966507970214
GO:0005515protein binding0.0204183646101707
GO:0016363nuclear matrix0.0220909551404238
GO:0044428nuclear part0.0236262360421581
GO:0048523negative regulation of cellular process0.0240742996074799
GO:0048519negative regulation of biological process0.0251846368767134
GO:0048468cell development0.0265674164750137
GO:0030155regulation of cell adhesion0.0265674164750137
GO:0051179localization0.0275572213624321
GO:0005200structural constituent of cytoskeleton0.0310461000661591
GO:0043229intracellular organelle0.0310461000661591
GO:0043226organelle0.0310461000661591
GO:0007165signal transduction0.0368719025886468
GO:0007154cell communication0.0422377920115624
GO:0050954sensory perception of mechanical stimulus0.0422377920115624
GO:0007605sensory perception of sound0.0422377920115624
GO:0048869cellular developmental process0.0422377920115624
GO:0030154cell differentiation0.0422377920115624
GO:0050794regulation of cellular process0.0431562287345324



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
somatic cell8.80e-48588
animal cell7.68e-36679
eukaryotic cell7.68e-36679
native cell1.17e-29722
mesodermal cell1.92e-24121
embryonic cell6.29e-20250
somatic stem cell2.09e-17433
contractile cell4.24e-1759
multi fate stem cell6.71e-17427
smooth muscle cell9.99e-1743
smooth muscle myoblast9.99e-1743
stem cell8.98e-16441
muscle precursor cell9.96e-1658
myoblast9.96e-1658
multi-potent skeletal muscle stem cell9.96e-1658
muscle cell3.26e-1555
vascular associated smooth muscle cell4.60e-1532
electrically responsive cell2.34e-1361
electrically active cell2.34e-1361
endothelial cell1.28e-1236
non-terminally differentiated cell2.75e-12106
meso-epithelial cell5.74e-1145
endothelial cell of vascular tree1.80e-0924
lining cell8.04e-0958
barrier cell8.04e-0958
blood vessel endothelial cell1.13e-0818
embryonic blood vessel endothelial progenitor cell1.13e-0818
fibroblast1.37e-0876
epithelial cell of nephron2.14e-0815
kidney cortical cell4.04e-0712
renal cortical epithelial cell4.04e-0712
Uber Anatomy
Ontology termp-valuen
vasculature2.61e-2378
vascular system2.61e-2378
vessel2.42e-2068
cardiovascular system5.12e-19109
epithelial tube open at both ends8.53e-1959
blood vessel8.53e-1959
blood vasculature8.53e-1959
vascular cord8.53e-1959
mesoderm2.77e-18315
mesoderm-derived structure2.77e-18315
presumptive mesoderm2.77e-18315
splanchnic layer of lateral plate mesoderm2.88e-1883
artery1.08e-1742
arterial blood vessel1.08e-1742
arterial system1.08e-1742
epithelial vesicle1.24e-1778
circulatory system1.75e-17112
lateral plate mesoderm1.82e-17203
epithelial tube4.86e-16117
multilaminar epithelium1.13e-1483
somite2.35e-1471
presomitic mesoderm2.35e-1471
presumptive segmental plate2.35e-1471
dermomyotome2.35e-1471
trunk paraxial mesoderm2.35e-1471
unilaminar epithelium7.77e-14148
paraxial mesoderm8.92e-1472
presumptive paraxial mesoderm8.92e-1472
dense mesenchyme tissue9.75e-1473
systemic artery9.12e-1333
systemic arterial system9.12e-1333
skeletal muscle tissue1.07e-1262
striated muscle tissue1.07e-1262
myotome1.07e-1262
muscle tissue2.00e-1264
musculature2.00e-1264
musculature of body2.00e-1264
musculoskeletal system6.93e-12167
trunk mesenchyme7.51e-10122
blood vessel endothelium1.13e-0818
endothelium1.13e-0818
cardiovascular system endothelium1.13e-0818
nephron epithelium2.14e-0815
renal tubule2.14e-0815
nephron tubule2.14e-0815
nephron2.14e-0815
uriniferous tubule2.14e-0815
nephrogenic mesenchyme2.14e-0815
simple squamous epithelium2.18e-0822
excretory tube1.83e-0716
kidney epithelium1.83e-0716
aorta1.93e-0721
aortic system1.93e-0721
mesenchyme1.93e-07160
entire embryonic mesenchyme1.93e-07160
parenchyma2.13e-0715
trunk3.97e-07199
cortex of kidney4.04e-0712
renal parenchyma4.04e-0712
squamous epithelium6.64e-0725
organism subdivision8.97e-07264


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.76953
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
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
MA0073.10.214613
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
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
MA0108.22.35545
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
MA0146.12.31379
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.6798
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCLAF1#9774210.82632380506090.01202203816432580.0436431451855824
CCNT2#90546.336201576962630.0006203100587215640.00511362871756425
CHD2#110637.758017125587640.003351522464536340.0172896841034187
E2F1#186944.907389214879320.001724022357361790.0106277399941275
E2F4#187439.501045236463330.001850751034728270.0109240752410978
ELF1#199744.258097958807540.003041525565781240.0160585353907602
ETS1#211349.728760922202340.0001115955317418140.0015434943371187
GABPB1#255335.300762877136630.01012678824234270.0378387763315099
GTF2B#2959215.97191496716210.005636585723537220.0254663166802433
GTF2F1#296239.554745657568240.001820362319304780.0108968200989208
HEY1#2346244.040111043105710.00375304636917980.0185597996946243
IRF1#365935.727872815172930.008097114790333330.0319875391151652
MYC#460945.22228187160940.001344309395272740.0088573799087054
NRF1#489939.157709585783180.002061953791733420.0119591487785221
PAX5#507946.669565531177830.0005052774169483260.00443190292673773
PBX3#5090210.95725634337210.01174530180688030.0428201059590455
RDBP#7936276.81920199501250.0002517810050617040.00271062327467677
SP1#666745.69838137814090.0009482606065333980.00683049792990838
TAF1#687243.343046285745290.008005664898701650.032131879495619
TBP#690843.706770687096390.005296377814784350.0243538239157426
YY1#752844.911170749853860.00171871838055440.0106636505047657
ZBTB7A#5134135.513931980906920.009038352821081090.0342261251008299
ZNF143#7702310.12565741417090.001534861610688180.00976126000235436



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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