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Coexpression cluster:C2721: Difference between revisions

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{{Coexpression_clusters
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mutase activity!0.00447427293064877!5238$GO:0006890!retrograde vesicle-mediated transport, Golgi to ER!0.0126741212418515!9276$GO:0030126!COPI vesicle coat!0.0126741212418515!9276$GO:0030663!COPI coated vesicle membrane!0.0126741212418515!9276$GO:0006891!intra-Golgi vesicle-mediated transport!0.0126741212418515!9276$GO:0030137!COPI-coated vesicle!0.0126741212418515!9276$GO:0016868!intramolecular transferase activity, phosphotransferases!0.0185286344708939!5238$GO:0006041!glucosamine metabolic process!0.0195651482442882!5238$GO:0006040!amino sugar metabolic process!0.0203707987891853!5238$GO:0030120!vesicle coat!0.0207290900904621!9276$GO:0030662!coated vesicle membrane!0.0207290900904621!9276$GO:0016866!intramolecular transferase activity!0.0237242956795106!5238$GO:0005798!Golgi-associated vesicle!0.0237242956795106!9276$GO:0048193!Golgi vesicle transport!0.0272703770303969!9276$GO:0030659!cytoplasmic vesicle membrane!0.0272703770303969!9276$GO:0044433!cytoplasmic vesicle part!0.0272703770303969!9276$GO:0012506!vesicle membrane!0.0272703770303969!9276$GO:0030117!membrane coat!0.0272703770303969!9276$GO:0048475!coated membrane!0.0272703770303969!9276$GO:0030135!coated vesicle!0.0327374462988358!9276$GO:0008565!protein transporter activity!0.0327374462988358!9276$GO:0045045!secretory 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|full_id=C2721_Preadipocyte_Smooth_Mast_Fibroblast_Mesenchymal_mesenchymal_Myoblast
|id=C2721
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2721_Preadipocyte_Smooth_Mast_Fibroblast_Mesenchymal_mesenchymal_Myoblast



Phase1 CAGE Peaks

Hg19::chr3:139108446..139108457,-p3@COPB2
Hg19::chr3:139108463..139108474,-p2@COPB2
Hg19::chr3:139108475..139108518,-p1@COPB2
Hg19::chr6:83902933..83903005,-p1@PGM3


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:0004610phosphoacetylglucosamine mutase activity0.00447427293064877
GO:0006890retrograde vesicle-mediated transport, Golgi to ER0.0126741212418515
GO:0030126COPI vesicle coat0.0126741212418515
GO:0030663COPI coated vesicle membrane0.0126741212418515
GO:0006891intra-Golgi vesicle-mediated transport0.0126741212418515
GO:0030137COPI-coated vesicle0.0126741212418515
GO:0016868intramolecular transferase activity, phosphotransferases0.0185286344708939
GO:0006041glucosamine metabolic process0.0195651482442882
GO:0006040amino sugar metabolic process0.0203707987891853
GO:0030120vesicle coat0.0207290900904621
GO:0030662coated vesicle membrane0.0207290900904621
GO:0016866intramolecular transferase activity0.0237242956795106
GO:0005798Golgi-associated vesicle0.0237242956795106
GO:0048193Golgi vesicle transport0.0272703770303969
GO:0030659cytoplasmic vesicle membrane0.0272703770303969
GO:0044433cytoplasmic vesicle part0.0272703770303969
GO:0012506vesicle membrane0.0272703770303969
GO:0030117membrane coat0.0272703770303969
GO:0048475coated membrane0.0272703770303969
GO:0030135coated vesicle0.0327374462988358
GO:0008565protein transporter activity0.0327374462988358
GO:0045045secretory pathway0.0486385500290966



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite5.47e-1271
presomitic mesoderm5.47e-1271
presumptive segmental plate5.47e-1271
dermomyotome5.47e-1271
trunk paraxial mesoderm5.47e-1271
dense mesenchyme tissue8.77e-1273
paraxial mesoderm1.61e-1172
presumptive paraxial mesoderm1.61e-1172
multilaminar epithelium6.12e-1183
unilaminar epithelium6.80e-11148
skeletal muscle tissue7.41e-1162
striated muscle tissue7.41e-1162
myotome7.41e-1162
artery2.36e-1042
arterial blood vessel2.36e-1042
arterial system2.36e-1042
muscle tissue2.36e-1064
musculature2.36e-1064
musculature of body2.36e-1064
surface structure5.90e-1099
trunk mesenchyme1.13e-09122
systemic artery2.23e-0933
systemic arterial system2.23e-0933
splanchnic layer of lateral plate mesoderm1.51e-0883
epithelial vesicle2.27e-0878
vasculature3.38e-0878
vascular system3.38e-0878
integument3.75e-0846
integumental system3.75e-0846
mesenchyme1.14e-07160
entire embryonic mesenchyme1.14e-07160
skin of body2.97e-0741
epithelial tube open at both ends5.29e-0759
blood vessel5.29e-0759
blood vasculature5.29e-0759
vascular cord5.29e-0759
vessel5.42e-0768
multi-cellular organism7.33e-07656
Disease
Ontology termp-valuen
ovarian cancer1.43e-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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.13.73908
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
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.13.20374
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
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.22.52211
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
MA0102.21.75932
MA0258.11.07498
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
BRCA1#672315.13817298241780.0004682184421431190.00430346439135662
CEBPB#105135.978360719368610.007153832484726970.0297368800347224
CHD2#110637.758017125587640.003351522464536340.0173050701870624
ELF1#199744.258097958807540.003041525565781240.0161163819667492
ELK4#2005312.1767612438510.0008912632577620610.00663880203818643
ETS1#211337.296570691651750.00400857377511390.0192094813480371
FOSL2#2355312.69765045342130.000787568572975710.00616819454015824
GABPB1#255347.067683836182170.0004006876864423170.00390732224877209
GATA1#2623310.17023110785030.001515158168498270.00966656102381131
GATA3#2625320.42738726790450.0001924415576258320.00232029598671025
HEY1#2346244.040111043105710.00375304636917980.0186418914558532
IRF1#365947.63716375356390.0002938853996185490.0030794719826188
JUN#372539.384621894252250.001918994502030470.0112879677159989
MXI1#460137.471178721569470.003741314738550960.0186394681095036
MYC#460945.22228187160940.001344309395272740.0088870951343771
NFKB1#479045.488063424193840.001102199566301980.00768749969981383
NRF1#489939.157709585783180.002061953791733420.011964464251061
PBX3#5090316.43588451505810.0003669431395554610.00365923561081188
POU2F2#545236.829593043306890.004860473775203740.0227694904731543
RFX5#599339.035933120396320.002144561191324070.012386673280649
SIN3A#2594245.408884726815140.001168172384885160.00797507881455228
SP1#666745.69838137814090.0009482606065333980.00685176349008866
SREBF1#6720335.25438708036623.78704019553645e-050.000725182785078164
STAT3#677437.889598747865680.003190760481680130.0167440374809663
TAF1#687243.343046285745290.008005664898701650.0322869800878708
TAF7#6879411.43306940492395.85061525419808e-050.00097097156607849
TBP#690843.706770687096390.005296377814784350.0244723444940168
ZBTB33#10009323.74854377248590.0001229451908818380.00165616829491917
ZBTB7A#5134147.35190930787590.000342223540015990.00347105800677187
ZNF143#7702310.12565741417090.001534861610688180.00977018417496577



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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