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Coexpression cluster:C3881: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3881_squamous_glioblastoma_chronic_somatostatinoma_smallcell_large_lung
|id=C3881
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3881_squamous_glioblastoma_chronic_somatostatinoma_smallcell_large_lung



Phase1 CAGE Peaks

Hg19::chr1:156631176..156631189,-p3@ENST00000448869
Hg19::chr1:156631192..156631208,-p2@ENST00000448869
Hg19::chr1:156631224..156631248,-p1@ENST00000448869


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
anatomical cluster4.92e-14373
anatomical conduit1.28e-09240
blood vessel endothelium3.71e-0918
endothelium3.71e-0918
cardiovascular system endothelium3.71e-0918
trunk region element7.62e-09101
simple squamous epithelium8.85e-0922
subdivision of digestive tract4.25e-08118
digestive system7.16e-08145
digestive tract7.16e-08145
primitive gut7.16e-08145
tube3.06e-07192
endoderm-derived structure4.02e-07160
endoderm4.02e-07160
presumptive endoderm4.02e-07160
squamous epithelium6.03e-0725
viscus6.53e-0718
Disease
Ontology termp-valuen
cancer3.20e-31235
disease of cellular proliferation3.88e-31239
carcinoma5.21e-29106
cell type cancer5.33e-24143
organ system cancer1.36e-12137
respiratory system cancer5.09e-0716


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.110.4901
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.94723
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BATF#10538324.35780179230366.91705216281876e-050.0010993912811332
BCL3#602334.54710280373832.42397750207122e-050.000527192391376127
CCNT2#90536.336201576962630.003930750035764890.0190092425905376
E2F6#187635.017155731697390.00791769806886330.0322346886763347
EBF1#187938.9064668465690.00141523283560980.00915544487848441
EGR1#195834.988179094810140.008056488137383440.0320757687015931
ELF1#199734.258097958807540.01295179875054610.0462452276823345
ELK4#2005316.2356816584680.0002336043955745990.00255764854485958
EP300#203336.77394172622320.003216880500103790.0167489796375861
ETS1#211339.728760922202340.001085840092584840.00762533979488083
FOS#235338.99795530889440.001372499272417130.00897798143003711
FOSL1#8061339.7135797163731.59554825631833e-050.000371212885590622
FOSL2#2355316.93020060456170.0002060162053171620.00243120073074792
FOXA1#3169311.08141974938550.000734755275698670.0058151793148449
GABPB1#255337.067683836182170.002832212825417420.0154171518437282
GTF2B#2959331.94382993432423.06634405746243e-050.00062781005100435
GTF2F1#2962312.73966087675770.0004835525047438590.00434050193751129
HDAC2#3066313.41562023662630.0004140761399857210.0039136378266035
HMGN3#932438.178547723350590.001827766942164210.0108744532113871
HNF4A#3172323.13229036295378.07584663437677e-050.00122859919395146
HNF4G#3174328.75342252644684.20470658818262e-050.000756999399005697
IRF1#365937.63716375356390.002244692747297240.0128133726407399
JUN#3725312.51282919233630.0005103313992726250.00444302275830558
JUNB#3726330.61063265982113.4847716247536e-050.000680654691822782
JUND#372736.994663941871030.002921845042734990.0156819247863816
MAFF#23764356.31535648994525.59409009993116e-060.000169051266188284
MAFK#7975327.10073313782995.02195559325033e-050.000857707310226446
MXI1#460139.96157162875930.001011470541259020.00720383059591864
MYC#460935.22228187160940.007020843755740150.0294608020011148
NFE2#4778377.2042606516292.17039522930409e-067.82984135935372e-05
NFKB1#479035.488063424193840.006049381815655430.0269685144254594
NR3C1#2908314.9730233311730.0002978331194675480.00309106560310755
REST#597839.650028716128020.001112636247114590.00767875616284944
RFX5#5993312.04791082719510.0005717246050312580.00484701242185726
RXRA#6256320.07461713913330.0001235730348432220.00165268846023707
SIN3A#2594235.408884726815140.006318961977991520.0276881086645461
SMARCA4#65973156.7659033078882.58908533335753e-071.34061221185189e-05
SMARCB1#6598318.25271578115740.000164397760679890.00203093656584422
SMARCC1#6599343.66335931963151.20046018043203e-050.000301817190139964
SMARCC2#6601394.15537442689761.19621075407887e-064.85546268733941e-05
SMC3#9126315.04493284493280.0002935825420371870.00309118531180782
SP1#666735.69838137814090.005403962701712170.0246606860353105
SPI1#668838.204323508522730.001810593189410520.0109089963141136
SRF#6722313.79717826216780.0003806615025800190.00375197307172089
TAF7#6879311.43306940492390.0006690181981945830.00543198255471073
TCF12#6938310.63446490218640.0008313523990202070.00629490416887344
TCF7L2#6934310.77017656313730.0008003181298398380.0061400444547376
TRIM28#10155318.59052504526250.0001555969297255280.00197093847708967
USF1#739136.361499277207960.00388404057290560.0190336577230522
USF2#7392312.99219738506960.0004558979393427810.00421694490187058
YY1#752834.911170749853860.008441455341808260.0329539548627486
ZBTB7A#5134137.35190930787590.002516255860282270.0140254707686406
ZEB1#6935316.88843201754390.0002075486917327580.00242843130359371



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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