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{{Coexpression_clusters
{
|full_id=C4062_argyrophil_somatostatinoma_MCF7_small_heart_neuroblastoma_cerebellum

Latest revision as of 12:38, 17 September 2013


Full id: C4062_argyrophil_somatostatinoma_MCF7_small_heart_neuroblastoma_cerebellum



Phase1 CAGE Peaks

Hg19::chr20:62130603..62130627,-p3@EEF1A2
Hg19::chr20:62130629..62130646,-p4@EEF1A2
Hg19::chr20:62130651..62130656,-p11@EEF1A2


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 cell1.68e-07253
Uber Anatomy
Ontology termp-valuen
central nervous system2.00e-2581
nervous system2.43e-2489
regional part of nervous system3.27e-2353
regional part of brain3.27e-2353
brain2.19e-2268
future brain2.19e-2268
neural tube3.74e-2256
neural rod3.74e-2256
future spinal cord3.74e-2256
neural keel3.74e-2256
regional part of forebrain3.04e-2041
forebrain3.04e-2041
anterior neural tube3.04e-2041
future forebrain3.04e-2041
neurectoderm3.95e-1986
neural plate4.88e-1882
presumptive neural plate4.88e-1882
telencephalon2.77e-1634
brain grey matter6.18e-1634
gray matter6.18e-1634
organ system subdivision7.02e-16223
adult organism7.27e-16114
cerebral hemisphere1.35e-1532
pre-chordal neural plate2.25e-1561
regional part of telencephalon2.99e-1532
ectoderm-derived structure2.31e-14171
ectoderm2.31e-14171
presumptive ectoderm2.31e-14171
cerebral cortex8.60e-1425
pallium8.60e-1425
ecto-epithelium1.21e-13104
regional part of cerebral cortex2.98e-1322
neocortex1.53e-1220
structure with developmental contribution from neural crest3.84e-11132
anatomical cluster5.73e-08373
organ part4.82e-07218
Disease
Ontology termp-valuen
cell type cancer1.72e-26143
cancer2.24e-22235
disease of cellular proliferation4.71e-21239
carcinoma2.21e-20106
organ system cancer3.14e-07137


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.111.4064
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.923
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0145.12.11725
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.25.50873
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.223.8753
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
CTCF#1066435.360256373075030.0064925092527670.0279917096206132
E2F1#186934.907389214879320.008460985347239390.0325940337383473
E2F6#187635.017155731697390.00791769806886330.0322862903566302
EBF1#187938.9064668465690.00141523283560980.00916111950652364
ELF1#199734.258097958807540.01295179875054610.0463069703094137
HDAC2#3066313.41562023662630.0004140761399857210.00391753763782668
MYC#460935.22228187160940.007020843755740150.0294963554851662
TCF7L2#6934310.77017656313730.0008003181298398380.00614636555352179
ZBTB7A#5134137.35190930787590.002516255860282270.0140457106249075



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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