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Coexpression cluster:C3982: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3982_adult_biphenotypic_NK_signet_acute_cord_neuroblastoma
|id=C3982
|ontology_enrichment_celltype=CL:0000548!3.52e-17!679;CL:0000004!3.52e-17!679;CL:0000255!3.52e-17!679;CL:0000012!7.26e-17!682;CL:0000066!5.08e-12!254;CL:0000003!7.18e-12!722;CL:0000055!4.87e-07!180;CL:0000063!7.84e-07!578
|ontology_enrichment_disease=DOID:162!1.91e-50!235;DOID:14566!1.13e-49!239;DOID:0050686!1.69e-27!137;DOID:2531!4.38e-24!51;DOID:0060083!4.38e-24!51;DOID:0050687!4.57e-23!143;DOID:305!1.75e-18!106;DOID:1240!1.31e-17!39;DOID:8692!2.55e-13!31;DOID:0060058!2.18e-07!10
|ontology_enrichment_uberon=
}}

Latest revision as of 12:36, 17 September 2013


Full id: C3982_adult_biphenotypic_NK_signet_acute_cord_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr1:45205560..45205575,+p2@KIF2C
Hg19::chr1:45205577..45205589,+p3@KIF2C
Hg19::chr1:45205591..45205598,+p5@KIF2C


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
animal cell1.26e-16679
eukaryotic cell1.26e-16679
epithelial cell1.29e-11253
native cell1.47e-11722
Disease
Ontology termp-valuen
cancer6.75e-49235
disease of cellular proliferation2.71e-48239
organ system cancer4.74e-26137
hematologic cancer1.60e-2351
immune system cancer1.60e-2351
cell type cancer2.07e-22143
leukemia3.80e-1739
carcinoma4.42e-17106
myeloid leukemia4.68e-1331
lymphoma1.85e-0710


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0060.10.492218
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
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
MA0162.12.05956
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.11.29138
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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013926230582587
CCNT2#90536.336201576962630.003930750035764890.0190233365609476
CTCFL#140690319.74647435897440.0001298372005551160.00171951146192947
E2F1#186934.907389214879320.008460985347239390.0325712071021133
E2F4#1874312.66806031528440.0004917987006298980.00437615783378086
E2F6#187635.017155731697390.00791769806886330.0322610981825068
EGR1#195834.988179094810140.008056488137383440.0320965693145218
ELF1#199734.258097958807540.01295179875054610.0462816200673447
ELK4#2005316.2356816584680.0002336043955745990.00255845317422562
ETS1#211339.728760922202340.001085840092584840.0076304705577626
GABPB1#255337.067683836182170.002832212825417420.0154259961029346
GTF2F1#2962312.73966087675770.0004835525047438590.00434423570261883
HMGN3#932438.178547723350590.001827766942164210.0108818921259086
IRF1#365937.63716375356390.002244692747297240.012821782204932
JUND#372736.994663941871030.002921845042734990.0156932154496374
MAX#414936.452555509007120.003721913834265510.0186755529420993
MYC#460935.22228187160940.007020843755740150.0294844947929449
NFKB1#479035.488063424193840.006049381815655430.026981183269783
NRF1#4899312.21027944771090.0005492172401020010.00471514174591146
PAX5#507936.669565531177830.003370290999677260.0173061518125421
REST#597839.650028716128020.001112636247114590.00768383369783777
RFX5#5993312.04791082719510.0005717246050312580.00485055613524448
SIN3A#2594235.408884726815140.006318961977991520.0277113613277118
SP1#666735.69838137814090.005403962701712170.0246800971053051
SPI1#668838.204323508522730.001810593189410520.01091403336655
SRF#6722313.79717826216780.0003806615025800190.00375338997998061
STAT3#6774310.51946499715420.0008589184530415310.0064313582102957
TAF7#6879311.43306940492390.0006690181981945830.00543705482851483
TFAP2A#7020316.5186343730450.0002218033880766340.00248390778976363
TFAP2C#7022310.80922860986020.0007916746575753130.00616245878829158
THAP1#55145331.36914460285133.23800758564397e-050.000647471327277562
USF1#739136.361499277207960.00388404057290560.0190506416847644
YY1#752834.911170749853860.008441455341808260.0329761419279264
ZBTB7A#5134137.35190930787590.002516255860282270.0140367079260773
ZNF143#7702313.50087655222790.0004062804962997170.00389422987821642



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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