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Coexpression cluster:C1755: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1755_Reticulocytes_hepatoblastoma_acute_bone_epidermoid_Myoblast_merkel
|id=C1755
}}

Latest revision as of 11:51, 17 September 2013


Full id: C1755_Reticulocytes_hepatoblastoma_acute_bone_epidermoid_Myoblast_merkel



Phase1 CAGE Peaks

Hg19::chr15:91537708..91537721,-p3@PRC1
Hg19::chr15:91537723..91537804,-p1@PRC1
Hg19::chr15:91537809..91537824,-p2@PRC1
Hg19::chr20:30327143..30327154,+p2@TPX2
Hg19::chr2:234763105..234763145,-p2@HJURP


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:0005819spindle0.000260211140050149
GO:0000278mitotic cell cycle0.00147177864353539
GO:0051231spindle elongation0.00147177864353539
GO:0000022mitotic spindle elongation0.00147177864353539
GO:0015630microtubule cytoskeleton0.00231158995183011
GO:0022402cell cycle process0.00281613787933062
GO:0007049cell cycle0.00404685512039531
GO:0007052mitotic spindle organization and biogenesis0.00404685512039531
GO:0044430cytoskeletal part0.00405237908315862
GO:0005876spindle microtubule0.00508305403775861
GO:0007051spindle organization and biogenesis0.00508305403775861
GO:0005856cytoskeleton0.00701625588815873
GO:0000922spindle pole0.00701625588815873
GO:0000910cytokinesis0.00714527213891618
GO:0000226microtubule cytoskeleton organization and biogenesis0.0199867284173438
GO:0043232intracellular non-membrane-bound organelle0.0217224388160334
GO:0043228non-membrane-bound organelle0.0217224388160334
GO:0007067mitosis0.0335824835975614
GO:0000087M phase of mitotic cell cycle0.0335824835975614
GO:0051301cell division0.0335824835975614
GO:0044446intracellular organelle part0.0335824835975614
GO:0044422organelle part0.0335824835975614
GO:0005874microtubule0.0369179559006534
GO:0000279M phase0.0369179559006534
GO:0007017microtubule-based process0.0369179559006534
GO:0022403cell cycle phase0.0415502081008049



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 cell2.50e-18253
animal cell1.04e-15679
eukaryotic cell1.04e-15679
embryonic cell3.61e-08250
native cell5.89e-08722
squamous epithelial cell8.95e-0863
Disease
Ontology termp-valuen
cancer7.45e-57235
disease of cellular proliferation2.80e-55239
cell type cancer3.13e-34143
carcinoma3.97e-25106
organ system cancer1.18e-22137
hematologic cancer1.40e-1151
immune system cancer1.40e-1151
leukemia4.97e-1039
disease of anatomical entity4.42e-0939
myeloid leukemia1.21e-0731
sarcoma1.97e-0720


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.12.35759
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
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
MA0145.10.143698
MA0146.12.33916
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.23.06493
MA0099.20.699641
MA0079.21.03616
MA0102.21.66336
MA0258.10.345771
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
ATF3#467313.47790471560530.0008241088551409360.00627325836166649
BRCA1#672312.11053838593430.001127176470125940.00772752943176333
CCNT2#90545.068961261570110.002709998091280770.0148947211164758
CEBPB#105146.376918100659850.001113944176677320.0076533922681404
CHD2#110648.275218267293490.0004028373567101730.00387831219556174
E2F1#186954.907389214879320.0003512818099256460.00352662894807503
E2F4#1874512.66806031528443.06319883889696e-060.000103432726652299
E2F6#187655.017155731697390.0003144978599297790.00322745818936879
EBF1#187935.34388010794140.01187615563868110.0432322697367801
ELF1#199754.258097958807540.0007142416939776840.00573055913630909
FOS#235358.99795530889441.69470025615156e-050.000389080677186663
FOSL2#2355413.54416048364945.7953819349229e-050.00096456397434488
GABPB1#255357.067683836182175.6685482528729e-050.00094813823027193
GATA1#2623410.84824651504040.0001390956917094380.00181564991206624
GTF2F1#2962410.19172870140610.000177833889427640.00215862314945761
HEY1#2346254.040111043105710.0009288852205177990.0067416152568213
HMGN3#932458.178547723350592.73180911341838e-050.000581785097871741
IRF1#365957.63716375356393.84754333311872e-050.000724024465166822
IRF3#3661218.79278088459580.004339629777121510.0205881073086578
JUN#372537.50769751540180.004511206552906030.02133716322535
JUND#372745.595731153496820.001849593301755460.0109333073829544
MAX#414956.452555509007128.93743970843928e-050.00130675803683283
MXI1#460147.969257303007440.0004668546380070170.00429470902306129
MYC#460955.22228187160940.0002573944848850610.00276478685661945
NANOG#79923317.54686708860760.0003794200090681830.00376031944648623
NFKB1#479055.488063424193840.0002008162847462320.00239009139175062
NFYA#4800518.42558069983054.70418681889082e-072.22307948949384e-05
NFYB#4801516.75979325353657.55590255814554e-073.32405605421299e-05
NRF1#489949.768223558168730.0002101297748106790.00244493577890514
PBX3#5090313.14870761204650.0008860469322808430.00660324358216633
POU2F2#545247.284899246194020.0006631223288743860.0054254471527859
REST#597847.720022972902420.0005286363773650570.00457265650286808
RFX5#599349.638328661756080.000221480125815720.00249607886695457
SIN3A#2594255.408884726815140.0002159522671657270.00248007904448223
SMARCB1#6598414.60217262492594.30486693344344e-050.000768277507966335
SP1#666755.69838137814090.000166391843712550.00204228437718827
SP2#6668420.92282439507571.03516506540382e-050.00026940344945355
SRF#672238.278306957300690.003404846073776150.0173598281145825
STAT1#6772416.56526999775942.61308619905866e-050.000563510447126754
STAT2#6773339.15826271186443.51160213487062e-050.000680423405127557
TAF1#687253.343046285745290.002394600090870310.0135307925602123
TAF7#687949.146455523939130.0002720662872412990.00290267963767433
TBP#690853.706770687096390.001428755106721120.00918658835134195
TCF7L2#693436.462105937882410.006930108755689190.0293215697753777
TFAP2A#702039.911180623826970.002021546977511280.0117456659128957
TFAP2C#702236.485537165916130.006858951517940.0290581712470443
THAP1#55145318.82148676171080.0003085221948150010.0031748693964217
USF1#739145.089199421766370.00266867775360040.0147187386939307
ZBTB33#10009318.99883501798870.0003000982363342370.0030985625016818
ZNF263#1012746.577473309608540.0009875103237900160.00709169983540573



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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