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Coexpression cluster:C2764: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma
|id=C2764
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma



Phase1 CAGE Peaks

Hg19::chr3:98620486..98620493,-p4@DCBLD2
Hg19::chr3:98620500..98620547,-p1@DCBLD2
Hg19::chr3:98620631..98620663,-p13@DCBLD2
Hg19::chr3:98620849..98620854,-p32@DCBLD2


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

No GOStat results

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
multilaminar epithelium4.47e-2083
cell layer9.22e-20309
epithelial vesicle1.38e-1978
epithelium3.42e-19306
unilaminar epithelium3.85e-19148
epithelial tube5.13e-19117
organism subdivision7.24e-19264
somite2.31e-1871
presomitic mesoderm2.31e-1871
presumptive segmental plate2.31e-1871
dermomyotome2.31e-1871
trunk paraxial mesoderm2.31e-1871
paraxial mesoderm1.39e-1772
presumptive paraxial mesoderm1.39e-1772
mesenchyme1.45e-17160
entire embryonic mesenchyme1.45e-17160
dense mesenchyme tissue1.57e-1773
trunk mesenchyme3.36e-17122
skeletal muscle tissue6.72e-1762
striated muscle tissue6.72e-1762
myotome6.72e-1762
vasculature1.11e-1678
vascular system1.11e-1678
artery1.64e-1642
arterial blood vessel1.64e-1642
arterial system1.64e-1642
muscle tissue3.93e-1664
musculature3.93e-1664
musculature of body3.93e-1664
trunk8.22e-16199
systemic artery2.23e-1333
systemic arterial system2.23e-1333
vessel5.19e-1368
epithelial tube open at both ends6.00e-1359
blood vessel6.00e-1359
blood vasculature6.00e-1359
vascular cord6.00e-1359
splanchnic layer of lateral plate mesoderm1.50e-1283
multi-cellular organism1.74e-12656
anatomical system5.71e-12624
anatomical group1.02e-11625
multi-tissue structure1.08e-11342
cardiovascular system3.45e-11109
circulatory system8.30e-11112
anatomical cluster9.45e-11373
surface structure3.45e-0999
primordium8.30e-09160
embryo2.43e-08592
anatomical conduit2.77e-08240
developing anatomical structure5.46e-08581
pigment epithelium of eye8.43e-0811
integument2.15e-0746
integumental system2.15e-0746
aorta6.35e-0721
aortic system6.35e-0721
Disease
Ontology termp-valuen
ovarian cancer2.08e-0814
female reproductive organ cancer9.87e-0727


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.524262
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
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.946082
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
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
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
MA0105.10.656404
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
MA0145.10.195821
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.21.13403
MA0138.22.1393
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
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
CCNT2#90546.336201576962630.0006203100587215640.00513145047309477
CHD2#1106410.34402283411698.73193255208051e-050.00129245224462406
E2F1#186944.907389214879320.001724022357361790.0106686716229489
E2F6#187645.017155731697390.00157802193473060.0099846742300575
EGR1#195844.988179094810140.001615011500076050.0101590186144939
ELF1#199744.258097958807540.003041525565781240.0161171996836281
EP300#203346.77394172622320.0004748459821442640.00434868813829926
FOS#235348.99795530889440.0001525147711168630.00195202085547476
HEY1#2346244.040111043105710.00375304636917980.0186445516696366
IRF1#365935.727872815172930.008097114790333330.0320166043837361
MYC#460945.22228187160940.001344309395272740.0088893458865955
NFYA#4800418.42558069983058.67100748407158e-060.000234974403380631
NFYB#4801312.56984494015230.000811456397697350.00619229100680356
PAX5#507935.002174148383370.01196533174786410.043515941164299
POU2F2#545249.106124057742520.000145395665174930.00188586411763592
RFX5#5993412.04791082719514.74457429336527e-050.000827795848020006
SP1#666745.69838137814090.0009482606065333980.006853185903103
SP2#6668426.15353049384462.13562021071447e-067.75798397171509e-05
TAF1#687243.343046285745290.008005664898701650.0322957100063927
TAF7#687938.574802053692940.00250055433515240.0140375937545141
TBP#690843.706770687096390.005296377814784350.024478842439185
ZNF263#1012748.221841637010680.0002187871180958320.00249589380959154



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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