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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0943309910362639

Latest revision as of 12:34, 17 September 2013


Full id: C3873_neuroblastoma_nonsmall_teratocarcinoma_acute_neuroectodermal_medulloblastoma_small



Phase1 CAGE Peaks

Hg19::chr1:153643418..153643429,-p2@ILF2
Hg19::chr1:153643442..153643475,-p1@ILF2
Hg19::chr1:156308018..156308101,-p1@CCT3


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
simple squamous epithelium4.58e-0822
squamous epithelium2.21e-0725
blood vessel endothelium2.68e-0718
endothelium2.68e-0718
cardiovascular system endothelium2.68e-0718
Disease
Ontology termp-valuen
cancer1.98e-43235
disease of cellular proliferation2.06e-43239
cell type cancer2.27e-21143
organ system cancer3.84e-21137
carcinoma7.76e-18106
hematologic cancer5.01e-1451
immune system cancer5.01e-1451
leukemia3.77e-1139
myeloid leukemia1.43e-0831


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.15.46492
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.12.86846
MA0078.11.04495
MA0081.11.70054
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
MA0100.13.60951
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
MA0119.11.66081
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
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
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
BDP1#558142700.1022727272732.7031542867596e-069.4199109294256e-05
BRCA1#672213.45615376214920.007119807716084560.0296261045483946
BRF1#297221184.788461538469.40380308868135e-074.02674780967114e-05
CEBPB#105137.971147625824820.001974187055288560.0115237045532798
CHD2#1106310.34402283411690.0009033701102746880.00660508757679769
CTCF#1066435.360256373075030.0064925092527670.0279524764551791
E2F1#186934.907389214879320.008460985347239390.0325460148311419
E2F6#187635.017155731697390.00791769806886330.0322321757401681
EP300#203336.77394172622320.003216880500103790.0167481446934367
FOS#235338.99795530889440.001372499272417130.00897741914648792
FOSL2#2355211.28680040304110.0100534586973120.0376753085108387
GATA2#2624312.7449317335540.0004829527704283790.0043692917871422
GATA3#2625218.15767757147070.003944546819279620.0189504818647934
GTF2B#2959221.29588662288280.002878180589911410.0155812929001533
GTF2F1#2962312.73966087675770.0004835525047438590.00434012891396905
HSF1#32973164.2906666666672.24910326529255e-071.1911465310542e-05
IRF1#365937.63716375356390.002244692747297240.0128119721190828
IRF3#3661346.98195221148969.63568551583244e-060.000253550355149414
MAX#414936.452555509007120.003721913834265510.0186585205652981
MEF2A#4205318.74323090964410.0001518243905622470.00195035516924114
MYC#460935.22228187160940.007020843755740150.0294596183610183
NFKB1#479035.488063424193840.006049381815655430.0269662122773161
NFYA#4800318.42558069983050.0001598135507814160.0019972199868446
NFYB#4801316.75979325353650.0002123649923296180.00245916259384776
PAX5#507936.669565531177830.003370290999677260.0172976471431173
POLR3A#111282226.0880733944952.5985838218527e-050.000561426346235983
POLR3G#1062221449.623529411766.26846128533636e-072.86257904756993e-05
PPARGC1A#108911116.6837121212120.008545763211786680.0325686383037436
RFX5#5993312.04791082719510.0005717246050312580.00484661899552431
RXRA#6256213.38307809275550.007196434429465730.0298308559388359
SIN3A#2594235.408884726815140.006318961977991520.0276857855442991
SP1#666735.69838137814090.005403962701712170.0246596085377777
STAT1#6772320.70658749719920.0001125992441046670.00154896634023278
TAF7#6879311.43306940492390.0006690181981945830.00543156029238527
TCF12#6938310.63446490218640.0008313523990202070.006294447817984
THAP1#55145220.91276306856750.002983447413736940.0158690228899044
TRIM28#10155212.39368336350830.008368344129438470.0329108861475533
USF1#739136.361499277207960.00388404057290560.0190327646691544
YY1#752834.911170749853860.008441455341808260.0329514914761021



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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