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Coexpression cluster:C2184: Difference between revisions

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{{Coexpression_clusters
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DNA N-glycosylase activity!0.0251497912781593!7374$GO:0006974!response to DNA damage stimulus!0.0251497912781593!11200;7374$GO:0009719!response to endogenous stimulus!0.0251497912781593!11200;7374$GO:0016605!PML body!0.0256508083652422!11200$GO:0019104!DNA N-glycosylase activity!0.0256508083652422!7374$GO:0008630!DNA damage response, signal transduction resulting in induction of apoptosis!0.0256508083652422!11200$GO:0016799!hydrolase activity, hydrolyzing N-glycosyl compounds!0.0256508083652422!7374$GO:0000077!DNA damage checkpoint!0.0256508083652422!11200$GO:0030532!small nuclear ribonucleoprotein complex!0.0256508083652422!6636$GO:0031570!DNA integrity checkpoint!0.0256508083652422!11200$GO:0006284!base-excision repair!0.0256508083652422!7374$GO:0044428!nuclear part!0.0256508083652422!11200;6636$GO:0008629!induction of apoptosis by intracellular signals!0.0256508083652422!11200$GO:0006950!response to stress!0.0265478637208075!11200;7374$GO:0042770!DNA damage response, signal transduction!0.0265478637208075!11200$GO:0000075!cell cycle 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0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.869502,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2184_diffuse_iPS_acute_Hodgkin_nonsmall_H9_HES3GFP
|id=C2184
}}

Latest revision as of 12:00, 17 September 2013


Full id: C2184_diffuse_iPS_acute_Hodgkin_nonsmall_H9_HES3GFP



Phase1 CAGE Peaks

Hg19::chr12:109535373..109535414,+p1@UNG
Hg19::chr12:96252710..96252789,+p1@SNRPF
Hg19::chr21:33651324..33651366,-p1@MIS18A
Hg19::chr22:29137782..29137837,-p1@CHEK2


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:0004844uracil DNA N-glycosylase activity0.0251497912781593
GO:0006974response to DNA damage stimulus0.0251497912781593
GO:0009719response to endogenous stimulus0.0251497912781593
GO:0016605PML body0.0256508083652422
GO:0019104DNA N-glycosylase activity0.0256508083652422
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0256508083652422
GO:0016799hydrolase activity, hydrolyzing N-glycosyl compounds0.0256508083652422
GO:0000077DNA damage checkpoint0.0256508083652422
GO:0030532small nuclear ribonucleoprotein complex0.0256508083652422
GO:0031570DNA integrity checkpoint0.0256508083652422
GO:0006284base-excision repair0.0256508083652422
GO:0044428nuclear part0.0256508083652422
GO:0008629induction of apoptosis by intracellular signals0.0256508083652422
GO:0006950response to stress0.0265478637208075
GO:0042770DNA damage response, signal transduction0.0265478637208075
GO:0000075cell cycle checkpoint0.0324006819574708
GO:0005634nucleus0.0350096761340437



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell3.05e-23253
animal cell6.88e-17679
eukaryotic cell6.88e-17679
native cell4.23e-10722
embryonic cell2.20e-08250
squamous epithelial cell4.14e-0763
Disease
Ontology termp-valuen
cancer7.54e-57235
disease of cellular proliferation3.44e-55239
cell type cancer2.04e-29143
organ system cancer1.15e-27137
hematologic cancer5.68e-2451
immune system cancer5.68e-2451
carcinoma1.45e-23106
leukemia3.35e-2139
myeloid leukemia9.83e-1831
germ cell and embryonal cancer8.40e-0822
germ cell cancer8.40e-0822


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
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.11.41335
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.13.69367
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
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
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
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0139.10.912459
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
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.12.08227
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
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
E2F1#186944.907389214879320.001724022357361790.0106296222315667
E2F4#1874412.66806031528443.88145892637771e-050.000725699407110565
E2F6#187645.017155731697390.00157802193473060.00995391875589352
ETS1#211337.296570691651750.00400857377511390.0191989102310887
HEY1#2346244.040111043105710.00375304636917980.0185624365292086
IRF1#365935.727872815172930.008097114790333330.0319948004838115
IRF3#3661223.49097610574480.002641101425375540.0145928468820652
JUNB#3726322.95797449486590.0001359772504018780.00177850069564455
MXI1#460137.471178721569470.003741314738550960.0186252523942763
MYC#460945.22228187160940.001344309395272740.00886017474017982
SIN3A#2594245.408884726815140.001168172384885160.00794650919722665
SREBF1#6720223.50292472024410.002638454900768240.0145813097354923
TAF1#687243.343046285745290.008005664898701650.0321368196316063
TAF7#6879411.43306940492395.85061525419808e-050.000967588925626593
TBP#690843.706770687096390.005296377814784350.0243570410655334



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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