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{{Coexpression_clusters
{
|full_id=C1675_Hodgkin_Burkitt_retinoblastoma_Reticulocytes_granulocyte_diffuse_MCF7
|

Latest revision as of 11:49, 17 September 2013


Full id: C1675_Hodgkin_Burkitt_retinoblastoma_Reticulocytes_granulocyte_diffuse_MCF7



Phase1 CAGE Peaks

Hg19::chr12:53662049..53662061,+p2@ESPL1
Hg19::chr12:53662073..53662105,+p1@ESPL1
Hg19::chr16:89883015..89883088,-p1@FANCA
Hg19::chr19:48673552..48673578,-p2@LIG1
Hg19::chr21:47743719..47743792,-p1@C21orf58


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:0051301cell division0.00408715906915419
GO:0045875negative regulation of sister chromatid cohesion0.00408715906915419
GO:0007063regulation of sister chromatid cohesion0.00408715906915419
GO:0045842positive regulation of mitotic metaphase/anaphase transition0.00408715906915419
GO:0051293establishment of spindle localization0.00408715906915419
GO:0051653spindle localization0.00408715906915419
GO:0040001establishment of mitotic spindle localization0.00408715906915419
GO:0003910DNA ligase (ATP) activity0.00474459431445905
GO:0006281DNA repair0.00474459431445905
GO:0003909DNA ligase activity0.00476807151383685
GO:0006974response to DNA damage stimulus0.00506629389735859
GO:0009719response to endogenous stimulus0.0064670891858124
GO:0007062sister chromatid cohesion0.00660116780290485
GO:0030071regulation of mitotic metaphase/anaphase transition0.00715063354999629
GO:0007091mitotic metaphase/anaphase transition0.00715063354999629
GO:0045840positive regulation of mitosis0.00715063354999629
GO:0016886ligase activity, forming phosphoric ester bonds0.00785121375196704
GO:0007049cell cycle0.0107858894254426
GO:0051656establishment of organelle localization0.0114369722282121
GO:0045787positive regulation of progression through cell cycle0.0114369722282121
GO:0000070mitotic sister chromatid segregation0.0125614912332567
GO:0000819sister chromatid segregation0.0125614912332567
GO:0051640organelle localization0.0134980059960521
GO:0000910cytokinesis0.0134980059960521
GO:0006950response to stress0.0163545176936061
GO:0006259DNA metabolic process0.0164194544395607
GO:0007059chromosome segregation0.0208051301178182
GO:0005634nucleus0.0218631855041171
GO:0007088regulation of mitosis0.0219915913189527
GO:0000226microtubule cytoskeleton organization and biogenesis0.0323303903291635
GO:0005813centrosome0.0395379803144608
GO:0005815microtubule organizing center0.0436237898276382



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 cell7.19e-17253
animal cell1.49e-09679
eukaryotic cell1.49e-09679
migratory neural crest cell1.73e-0741
embryonic cell4.09e-07250
Disease
Ontology termp-valuen
cancer1.18e-41235
disease of cellular proliferation3.70e-40239
hematologic cancer5.78e-2351
immune system cancer5.78e-2351
organ system cancer1.03e-22137
cell type cancer1.69e-19143
leukemia1.24e-1839
carcinoma1.64e-15106
myeloid leukemia2.78e-1431


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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.11.73592
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.13.25531
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.946108
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.12.27598
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.340387
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
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#90556.336201576962639.78880505817628e-050.00138903941775934
CHD2#1106510.34402283411698.43981772346334e-060.000230082517154996
CTBP2#1488225.08680013573130.002461438599678380.0138462881564048
CTCF#1066444.288205098460020.005152015588243280.023923852030614
E2F1#186954.907389214879320.0003512818099256460.00352391902284358
E2F4#1874512.66806031528443.06319883889696e-060.000103365888056724
E2F6#187655.017155731697390.0003144978599297790.00322523978723548
EGR1#195854.988179094810140.0003237398000590710.00330508904969397
ELF1#199754.258097958807540.0007142416939776840.00572703940708909
ETS1#211335.83725655332140.009253279045631430.0349677320348338
FOS#235347.198364247115530.0006947858453382510.00559509128701377
IRF1#365957.63716375356393.84754333311872e-050.000723503021547689
MXI1#460147.969257303007440.0004668546380070170.00429395257937603
NFYA#4800414.74046455986444.14733626928016e-050.000752116083742577
NFYB#4801413.40783460282926.03169250119439e-050.00099125717251336
NRF1#489937.326167668626540.004839689817117540.0226863718496382
PAX5#507956.669565531177837.57493746384605e-050.00116960214930014
PBX3#5090417.53161014939532.08739444052064e-050.000460704539250919
RAD21#588536.21302033727380.007751055068811640.0318868885780761
SIN3A#2594255.408884726815140.0002159522671657270.00247817150099125
SIX5#147912310.25202921327540.001832291068677690.0108482226146049
SMARCB1#6598310.95162946869440.001511872848343180.00965090693772468
SMARCC1#6599217.46534372785260.005008037385199390.0233768846193277
SMC3#912639.02695970695970.002650964449467550.0146349548650989
SP1#666755.69838137814090.000166391843712550.00204084530422725
TAF1#687253.343046285745290.002394600090870310.0135205513807863
TAL1#6886211.94744667097610.0104757781809920.0388026598611371
TFAP2A#702039.911180623826970.002021546977511280.0117443591691773
TFAP2C#702236.485537165916130.006858951517940.0290546354728102
YY1#752854.911170749853860.00034993140821360.00352527118186748
ZNF143#770238.100525931336740.003624870512090980.01832774261291
ZNF263#1012746.577473309608540.0009875103237900160.00709023722716249



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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