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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.162521694715315,

Latest revision as of 11:44, 17 September 2013


Full id: C1437_Mesenchymal_Osteoblast_Renal_Pericytes_Placental_Fibroblast_Nucleus



Phase1 CAGE Peaks

Hg19::chr17:79791135..79791175,-p1@FAM195B
Hg19::chr19:507487..507508,+p1@TPGS1
Hg19::chr1:36789194..36789256,-p1@FAM176B
Hg19::chr1:36789257..36789268,-p2@FAM176B
Hg19::chr3:49395753..49395769,-p3@GPX1
Hg19::chr6:144416737..144416766,-p2@SF3B5


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:0010269response to selenium ion0.00356170431735566
GO:0033598mammary gland epithelial cell proliferation0.00356170431735566
GO:0033599regulation of mammary gland epithelial cell proliferation0.00356170431735566
GO:0008539proteasome inhibitor activity0.00356170431735566
GO:0043295glutathione binding0.00427398227263908
GO:0008631induction of apoptosis by oxidative stress0.00474879929383486
GO:0009650UV protection0.00610541935439425
GO:0030503regulation of cell redox homeostasis0.00712267470585477
GO:0043154negative regulation of caspase activity0.00712267470585477
GO:0042744hydrogen peroxide catabolic process0.00771577659443147
GO:0042743hydrogen peroxide metabolic process0.00771577659443147
GO:0001836release of cytochrome c from mitochondria0.00771577659443147
GO:0004602glutathione peroxidase activity0.0083782604577414
GO:0006749glutathione metabolic process0.0083782604577414
GO:0008637apoptotic mitochondrial changes0.0083782604577414
GO:0017124SH3 domain binding0.0083782604577414
GO:0042542response to hydrogen peroxide0.0083782604577414
GO:0000302response to reactive oxygen species0.0106811811903355
GO:0050678regulation of epithelial cell proliferation0.0111441033976822
GO:0009411response to UV0.0111441033976822
GO:0050673epithelial cell proliferation0.0111441033976822
GO:0010038response to metal ion0.0111441033976822
GO:0008629induction of apoptosis by intracellular signals0.0111441033976822
GO:0010035response to inorganic substance0.0123917946099916
GO:0006800oxygen and reactive oxygen species metabolic process0.0123917946099916
GO:0060047heart contraction0.0123917946099916
GO:0003015heart process0.0123917946099916
GO:0008430selenium binding0.0127113856780267
GO:0043281regulation of caspase activity0.0147255051928963
GO:0040029regulation of gene expression, epigenetic0.0149003678103095
GO:0004601peroxidase activity0.0149003678103095
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0149003678103095
GO:0009416response to light stimulus0.0174643995027196
GO:0006790sulfur metabolic process0.0175880982868606
GO:0008632apoptotic program0.0175880982868606
GO:0007005mitochondrion organization and biogenesis0.0175880982868606
GO:0009314response to radiation0.0194166461393986
GO:0045454cell redox homeostasis0.0202138906401953
GO:0006979response to oxidative stress0.0218801128957829
GO:0019904protein domain specific binding0.0225752112702164
GO:0005681spliceosome0.0241013951022955
GO:0008015blood circulation0.0264440662770201
GO:0003013circulatory system process0.0264440662770201
GO:0009628response to abiotic stimulus0.0266486946639436
GO:0006916anti-apoptosis0.0268441119592487
GO:0042277peptide binding0.0315119562790315
GO:0006917induction of apoptosis0.0315119562790315
GO:0012502induction of programmed cell death0.0315119562790315
GO:0008380RNA splicing0.0320173688309457
GO:0043066negative regulation of apoptosis0.0320173688309457
GO:0043069negative regulation of programmed cell death0.0320173688309457
GO:0043065positive regulation of apoptosis0.0345455564991135
GO:0043068positive regulation of programmed cell death0.0345455564991135
GO:0006397mRNA processing0.0358691419109499
GO:0006732coenzyme metabolic process0.0371437391052508
GO:0051336regulation of hydrolase activity0.0388762339987535
GO:0016071mRNA metabolic process0.0419149300765837
GO:0051186cofactor metabolic process0.0419149300765837
GO:0019725cellular homeostasis0.0450273350297991
GO:0004857enzyme inhibitor activity0.0473285241774172



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
epithelial vesicle8.53e-2678
somite2.78e-2271
presomitic mesoderm2.78e-2271
presumptive segmental plate2.78e-2271
dermomyotome2.78e-2271
trunk paraxial mesoderm2.78e-2271
dense mesenchyme tissue3.43e-2273
paraxial mesoderm1.16e-2172
presumptive paraxial mesoderm1.16e-2172
multilaminar epithelium2.90e-2083
vasculature5.77e-1978
vascular system5.77e-1978
skeletal muscle tissue7.40e-1962
striated muscle tissue7.40e-1962
myotome7.40e-1962
mesoderm1.92e-18315
mesoderm-derived structure1.92e-18315
presumptive mesoderm1.92e-18315
muscle tissue1.37e-1764
musculature1.37e-1764
musculature of body1.37e-1764
splanchnic layer of lateral plate mesoderm1.98e-1783
vessel7.22e-1668
cardiovascular system3.14e-15109
epithelial tube open at both ends3.96e-1559
blood vessel3.96e-1559
blood vasculature3.96e-1559
vascular cord3.96e-1559
circulatory system9.18e-15112
artery3.96e-1442
arterial blood vessel3.96e-1442
arterial system3.96e-1442
musculoskeletal system1.16e-13167
mesenchyme6.44e-13160
entire embryonic mesenchyme6.44e-13160
epithelial tube1.06e-12117
unilaminar epithelium1.58e-12148
trunk mesenchyme4.90e-12122
lateral plate mesoderm3.09e-11203
systemic artery1.29e-1033
systemic arterial system1.29e-1033
trunk5.98e-08199
organism subdivision6.00e-07264
adipose tissue9.22e-0714


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)
MA0003.13.05245
MA0004.11.37419
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.13.70108
MA0017.11.935
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.12.77054
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.12.41676
MA0042.13.39167
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.13.00536
MA0059.11.15845
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.720548
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.12.7063
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.11.54633
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.865577
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
MA0146.11.44958
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.23.52102
MA0035.20.621793
MA0039.22.28878
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.680553
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.11.60684
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.24.35479
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
ATF3#467311.23158726300440.001593459971184230.0100409898594491
CCNT2#90544.224134384641760.007109805478875810.0296128005746086
EGR1#195854.156815912341780.001617966818864440.0101342711164318
ELF1#199764.258097958807540.0001677224776288830.00205282641990893
ELK4#200538.117840829234010.004056113134185760.019408796830442
ETS1#211358.107300768501956.29183579217211e-050.00102754188944279
GABPB1#255344.711789224121450.004730054311555960.0222894979129447
MXI1#460146.64104775250620.001288516958039140.00863911039228667
NFKB1#479043.658708949462560.01207927289015230.0438341619657615
POLR2A#543062.147453176558070.01019570676818780.0380269059053913
SIN3A#2594265.408884726815143.99207083571449e-050.000742789748817362
SP1#666743.79892091876060.01052246616798510.0389493476561472
SREBF1#6720215.66861648016280.006411283165809460.0278913651249208
TAF1#687263.343046285745290.0007162474284635620.00573211993726483
TAF7#687935.716534702461960.01092729379889660.0402140891878841
THAP1#55145315.68457230142570.0006023469800864850.00503187620006818
ZNF263#1012745.481227758007120.002675609380607230.0147468451159026



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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