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{{Coexpression_clusters
{
|full_id=C1332_lymphoma_Reticulocytes_chronic_embryonic_Renal_Hodgkin_Alveolar
 

Latest revision as of 11:42, 17 September 2013


Full id: C1332_lymphoma_Reticulocytes_chronic_embryonic_Renal_Hodgkin_Alveolar



Phase1 CAGE Peaks

Hg19::chr11:118966167..118966182,-p1@H2AFX
Hg19::chr16:29802036..29802086,+p1@KIF22
Hg19::chr19:36545781..36545828,+p1@WDR62
Hg19::chr22:35796108..35796172,+p1@MCM5
Hg19::chr22:42343092..42343107,-p2@CENPM
Hg19::chr22:42343117..42343181,-p1@CENPM


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:0044427chromosomal part0.000875186642580658
GO:0005694chromosome0.000875186642580658
GO:0000775chromosome, pericentric region0.00112284037717332
GO:0000279M phase0.0136644533982684
GO:0022403cell cycle phase0.015865546315125
GO:0005634nucleus0.019196970695774
GO:0000724double-strand break repair via homologous recombination0.0201244507432831
GO:0000725recombinational repair0.0201244507432831
GO:0022402cell cycle process0.0246058068434886
GO:0043232intracellular non-membrane-bound organelle0.0246058068434886
GO:0043228non-membrane-bound organelle0.0246058068434886
GO:0007049cell cycle0.0273338469233302
GO:0000776kinetochore0.0273338469233302
GO:0005657replication fork0.0273338469233302
GO:0003677DNA binding0.0273338469233302
GO:0006302double-strand break repair0.0273338469233302
GO:0006270DNA replication initiation0.0273338469233302
GO:0043231intracellular membrane-bound organelle0.0273338469233302
GO:0043227membrane-bound organelle0.0273338469233302
GO:0003684damaged DNA binding0.0328162701163738
GO:0044446intracellular organelle part0.0338266050298457
GO:0044422organelle part0.0338266050298457
GO:0006259DNA metabolic process0.0365414791603242
GO:0051327M phase of meiotic cell cycle0.0365414791603242
GO:0007126meiosis0.0365414791603242
GO:0051321meiotic cell cycle0.0365414791603242
GO:0008094DNA-dependent ATPase activity0.039664069222455
GO:0043229intracellular organelle0.039664069222455
GO:0043226organelle0.039664069222455
GO:0006996organelle organization and biogenesis0.0432719300434897



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>

Cell Type
Ontology termp-valuen
animal cell1.15e-17679
eukaryotic cell1.15e-17679
epithelial cell2.88e-15253
native cell2.58e-13722
embryonic cell1.73e-08250
migratory neural crest cell2.90e-0841
neurectodermal cell6.44e-0759
epithelial cell of nephron6.94e-0715
kidney cell9.00e-0717
kidney epithelial cell9.00e-0717
Uber Anatomy
Ontology termp-valuen
nephron epithelium6.94e-0715
renal tubule6.94e-0715
nephron tubule6.94e-0715
nephron6.94e-0715
uriniferous tubule6.94e-0715
nephrogenic mesenchyme6.94e-0715
Disease
Ontology termp-valuen
cancer1.10e-31235
disease of cellular proliferation5.08e-30239
hematologic cancer1.36e-2151
immune system cancer1.36e-2151
organ system cancer2.90e-18137
leukemia3.67e-1739
cell type cancer2.10e-13143
myeloid leukemia7.34e-1331
carcinoma1.23e-11106


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)
MA0003.11.37104
MA0004.12.35384
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.15.03465
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.14.08025
MA0059.14.07239
MA0060.15.78054
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.12.7063
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
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
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.11.8938
MA0147.12.3862
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.21.50688
MA0039.20.200862
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.22.08061
MA0047.20.695777
MA0112.20.680553
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.10486
MA0102.21.58513
MA0258.10.289793
MA0259.11.6038
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
BHLHE40#8553214.95727118232580.00701655948451940.0296369188709747
CHD2#110646.896015222744570.001115391320135990.00765930397025989
E2F1#186964.907389214879327.15746523583771e-050.00112645948126229
E2F4#1874612.66806031528442.41728555395527e-071.26800043179073e-05
E2F6#187665.017155731697396.26776799983417e-050.00102457258120939
EGR1#195854.156815912341780.001617966818864440.0101294111374765
ELF1#199764.258097958807540.0001677224776288830.00205114377530245
ELK4#200538.117840829234010.004056113134185760.0194070184909853
FOS#235345.998636872596270.001899823711886350.0111821285305285
GATA1#262349.04020542920030.0003927397840144870.00384093550919458
GTF2F1#296236.369830438378830.008068208196303160.0319131796626915
HEY1#2346264.040111043105710.0002298968555807510.00252925289160413
IRF1#365945.091442502375930.003535240765893810.0179431895003734
IRF3#3661215.66065073716320.006417620989932530.027911960961461
MXI1#460169.96157162875931.02262624227062e-064.29959992417476e-05
NFKB1#479054.57338618682820.00102196259371130.00724299343950964
NFYA#4800412.28372046655370.0001190302509245860.00161593661462535
NFYB#4801411.17319550235760.0001723343348218770.00209894176028712
PAX5#507955.557971275981520.0003977176196612860.00388525212606913
POLR2A#543062.147453176558070.01019570676818780.0379929860192945
POU2F2#545257.588436714785448.70203885493171e-050.00129022180007128
RFX5#599336.023955413597550.009437904036335060.0356010134594141
SIN3A#2594265.408884726815143.99207083571449e-050.000742260790477453
SP1#666765.69838137814092.91961319085282e-050.000608990377550386
SP2#6668313.07676524692230.001024340397937320.0072583680589033
TAF1#687263.343046285745290.0007162474284635620.00572597712655435
TFAP2C#702247.206152406573480.0009421413689212550.00681745322724084
USF1#739155.30124939767330.0005003327549858890.0044103859383838
YY1#752864.911170749853867.12445972864136e-050.00112363553246689
ZEB1#693538.444216008771930.003623843810733590.0183340901879187



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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