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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.117986819981215

Latest revision as of 12:41, 17 September 2013


Full id: C4185_teratocarcinoma_iPS_H9_HES3GFP_NK_diffuse_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr2:219433617..219433629,+p5@RQCD1
Hg19::chr2:219433630..219433644,+p4@RQCD1
Hg19::chr2:219433648..219433655,+p6@RQCD1


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>

Cell Type
Ontology termp-valuen
epithelial cell4.67e-08253
Uber Anatomy
Ontology termp-valuen
central nervous system5.40e-1381
nervous system7.62e-1389
neural tube1.44e-1156
neural rod1.44e-1156
future spinal cord1.44e-1156
neural keel1.44e-1156
brain5.63e-1168
future brain5.63e-1168
regional part of nervous system8.82e-1153
regional part of brain8.82e-1153
neural plate3.53e-0982
presumptive neural plate3.53e-0982
pre-chordal neural plate9.74e-0961
regional part of forebrain1.17e-0841
forebrain1.17e-0841
anterior neural tube1.17e-0841
future forebrain1.17e-0841
neurectoderm1.35e-0886
organ system subdivision1.46e-07223
brain grey matter2.06e-0734
gray matter2.06e-0734
anatomical cluster2.09e-07373
telencephalon4.24e-0734
ecto-epithelium7.41e-07104
Disease
Ontology termp-valuen
disease of cellular proliferation6.41e-22239
cancer8.02e-22235
cell type cancer7.67e-13143
carcinoma3.01e-11106
organ system cancer7.24e-11137
hematologic cancer3.12e-0751
immune system cancer3.12e-0751


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.111.3843
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.13.88968
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
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.26659
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
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
MA0092.11.84783
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
MA0114.110.0093
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
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
MA0145.10.752137
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.29.27264
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
BCL3#602334.54710280373832.42397750207122e-050.000527521955279884
CEBPB#105137.971147625824820.001974187055288560.0115469378285888
CHD2#1106310.34402283411690.0009033701102746880.00661620413372918
E2F1#186934.907389214879320.008460985347239390.0326241175766202
E2F4#1874312.66806031528440.0004917987006298980.00437876935166973
E2F6#187635.017155731697390.00791769806886330.0323115219058305
EGR1#195834.988179094810140.008056488137383440.0321394791665466
ELF1#199734.258097958807540.01295179875054610.0463498118732279
EP300#203336.77394172622320.003216880500103790.0167807693197313
GABPB1#255337.067683836182170.002832212825417420.0154453279345084
HNF4A#3172323.13229036295378.07584663437677e-050.00123021199919439
HNF4G#3174328.75342252644684.20470658818262e-050.000758044797795969
IRF1#365937.63716375356390.002244692747297240.0128386344926055
MAX#414936.452555509007120.003721913834265510.0186980113972223
MYC#460935.22228187160940.007020843755740150.0295201055197772
NFKB1#479035.488063424193840.006049381815655430.0270146400754794
NR2C2#7182332.61461090524092.88098172333076e-050.000605527973843714
NRF1#4899312.21027944771090.0005492172401020010.00472096290856073
PAX5#507936.669565531177830.003370290999677260.017327450118898
POU2F2#545239.106124057742520.001324165192682130.00883614392425589
REST#597839.650028716128020.001112636247114590.00769248093554883
RXRA#6256320.07461713913330.0001235730348432220.00165459540846042
SETDB1#9869340.32002617801051.52461559299059e-050.000359515303491407
SIN3A#2594235.408884726815140.006318961977991520.0277474802396341
SIX5#147912317.0867153554590.0002004060546325010.00239970281354778
SP1#666735.69838137814090.005403962701712170.0247092710741262
TAF7#6879311.43306940492390.0006690181981945830.00544298446687264
YY1#752834.911170749853860.008441455341808260.0330131868355406
ZBTB7A#5134137.35190930787590.002516255860282270.0140539732494796



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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