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Coexpression cluster:C1724: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1724_Mast_medulloblastoma_small_non_cerebellum_hepatoblastoma_merkel
|id=C1724
}}

Latest revision as of 11:50, 17 September 2013


Full id: C1724_Mast_medulloblastoma_small_non_cerebellum_hepatoblastoma_merkel



Phase1 CAGE Peaks

Hg19::chr14:39644395..39644417,+p2@PNN
Hg19::chr14:39644425..39644470,+p1@PNN
Hg19::chr14:73525265..73525286,+p2@RBM25
Hg19::chr17:48796951..48796996,+p1@LUC7L3
Hg19::chr1:71546690..71546730,-p1@ZRANB2


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

p.valueFDRnGenesnPathwayName
4.41326987260908e-060.00279359982936155225{BCLAF1,25} (Static Module):NA



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:0008380RNA splicing2.07888694300519e-05
GO:0006397mRNA processing2.07888694300519e-05
GO:0016071mRNA metabolic process2.73085205460659e-05
GO:0006396RNA processing7.43177090078823e-05
GO:0016070RNA metabolic process0.029620301332372
GO:0003723RNA binding0.0328230854762404
GO:0003729mRNA binding0.0347091582755624
GO:0010467gene expression0.041196620178578
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.041196620178578
GO:0000375RNA splicing, via transesterification reactions0.041196620178578
GO:0000398nuclear mRNA splicing, via spliceosome0.041196620178578
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.041196620178578
GO:0003676nucleic acid binding0.041196620178578
GO:0016607nuclear speck0.0423044908580203



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>

Disease
Ontology termp-valuen
cancer3.02e-23235
disease of cellular proliferation7.60e-22239
organ system cancer9.31e-14137
hematologic cancer1.39e-1351
immune system cancer1.39e-1351
leukemia1.79e-1239
cell type cancer2.11e-12143
carcinoma1.60e-10106
myeloid leukemia2.08e-1031


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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.10.195817
MA0050.10.613347
MA0051.11.73592
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.11.29682
MA0060.13.25531
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
MA0073.10.00220137
MA0074.10.730989
MA0076.11.33654
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
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
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
MA0139.12.13391
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.11.35428
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.22.17426
MA0035.20.691506
MA0039.20.311551
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
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
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
BCLAF1#9774312.99158856607310.0009178032402542550.00667556602889576
CHD2#110636.206413700470110.007774550126275590.0319508220453349
E2F1#186954.907389214879320.0003512818099256460.00352527346467037
E2F4#187437.600836189170660.004354147360375710.0206485399886609
E2F6#187644.013724585357910.006632118233933880.0282911324688078
EGR1#195854.988179094810140.0003237398000590710.00330670523015837
ELF1#199754.258097958807540.0007142416939776840.0057287987310756
ELK4#2005412.98854532677446.83810524411663e-050.00109082766700824
ETS1#211347.783008737761870.0005121035947688870.00443994581886666
FOS#235347.198364247115530.0006947858453382510.00559595426091475
FOSL2#2355310.1581203627370.001881990703415430.011090290982001
FOXA1#316936.648851849631270.006389025166568720.0278061174051452
GABPB1#255357.067683836182175.6685482528729e-050.000947986406696225
GATA1#262338.136184886280260.003579251883681530.01813044366475
GATA3#2625210.89460654288240.0125158291218830.0452814867378094
GTF2B#2959319.16629796059450.0002924229654472410.00310211905417414
GTF2F1#2962512.73966087675772.97806917252935e-060.000101048267157177
HEY1#2346254.040111043105710.0009288852205177990.00673974180531183
HSF1#3297265.71626666666670.0003656829805786070.00364945674234584
IRF3#3661218.79278088459580.004339629777121510.0205862370227468
JUN#372537.50769751540180.004511206552906030.021335230773851
MAX#414956.452555509007128.93743970843928e-050.00130639225431727
MXI1#460135.976942977255580.008653004889366880.0329484897783501
MYC#460955.22228187160940.0002573944848850610.00276364990304419
NFKB1#479055.488063424193840.0002008162847462320.00238927454575207
NFYA#4800311.05534841989830.001470892907644430.00941117345962606
POU2F2#545247.284899246194020.0006631223288743860.00542417237666917
RFX5#599349.638328661756080.000221480125815720.00249580954467716
SIN3A#2594255.408884726815140.0002159522671657270.00247898866020239
SIX5#147912517.0867153554596.86007756253503e-073.09887387782697e-05
SP1#666755.69838137814090.000166391843712550.00204180446075608
SP2#6668420.92282439507571.03516506540382e-050.000269336333497034
SREBF1#6720328.2035096642939.31681575395428e-050.00135464140404738
SRF#6722411.03774260973420.0001299255814846750.00171027196933173
TAF1#687253.343046285745290.002394600090870310.0135271332156212
TAF7#6879511.43306940492395.11611886715123e-060.000157338733323442
TBP#690853.706770687096390.001428755106721120.00918319617150885
TCF12#693836.380678941311850.007185168653258840.0298279604490699
TCF7L2#693436.462105937882410.006930108755689190.0293180065757452
USF1#739145.089199421766370.00266867775360040.0147164071972265
YY1#752854.911170749853860.00034993140821360.00352629161929951
ZBTB33#10009318.99883501798870.0003000982363342370.00309825619854799
ZNF143#770238.100525931336740.003624870512090980.018328629940076



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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