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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:22, 17 September 2013


Full id: C3251_granulocyte_Burkitt_acute_signet_diffuse_splenic_biphenotypic



Phase1 CAGE Peaks

Hg19::chr12:125478179..125478208,+p1@BRI3BP
Hg19::chr12:125478212..125478235,+p3@BRI3BP
Hg19::chr12:125478241..125478260,+p2@BRI3BP


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 cell4.42e-09253
lymphocyte of B lineage1.73e-0824
pro-B cell1.73e-0824
Uber Anatomy
Ontology termp-valuen
organ system subdivision8.90e-11223
neural tube2.14e-0956
neural rod2.14e-0956
future spinal cord2.14e-0956
neural keel2.14e-0956
telencephalon5.69e-0934
regional part of nervous system5.97e-0953
regional part of brain5.97e-0953
brain grey matter9.62e-0934
gray matter9.62e-0934
cerebral hemisphere1.33e-0832
organ part1.54e-08218
regional part of telencephalon1.95e-0832
neural plate2.94e-0882
presumptive neural plate2.94e-0882
pre-chordal neural plate3.27e-0861
regional part of forebrain4.78e-0841
forebrain4.78e-0841
anterior neural tube4.78e-0841
future forebrain4.78e-0841
neurectoderm7.00e-0886
ecto-epithelium1.35e-07104
cerebral cortex1.65e-0725
pallium1.65e-0725
brain3.10e-0768
future brain3.10e-0768
central nervous system5.36e-0781
regional part of cerebral cortex5.57e-0722
nervous system6.71e-0789
neocortex7.95e-0720
Disease
Ontology termp-valuen
cancer1.69e-25235
disease of cellular proliferation1.28e-24239
hematologic cancer2.52e-1951
immune system cancer2.52e-1951
carcinoma6.33e-17106
leukemia6.45e-1539
cell type cancer1.68e-14143
organ system cancer2.84e-14137
myeloid leukemia1.13e-1131
lymphoma8.60e-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)
MA0003.16.06693
MA0004.10.826076
MA0006.10.639288
MA0007.13.13838
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
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
MA0073.10.211629
MA0074.10.935474
MA0076.11.74184
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.24.04548
MA0138.21.04628
MA0002.21.20011
MA0137.22.70092
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.12.08673
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
MA0162.14.34338
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
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
CCNT2#90536.336201576962630.003930750035764890.0189355905436001
E2F1#186934.907389214879320.008460985347239390.0323956757957376
E2F6#187635.017155731697390.00791769806886330.0320783795722715
EBF1#187938.9064668465690.00141523283560980.00912943187882967
EGR1#195834.988179094810140.008056488137383440.0319369758058221
ELF1#199734.258097958807540.01295179875054610.046045304479977
IRF1#365937.63716375356390.002244692747297240.0127735773897988
ZBTB7A#5134137.35190930787590.002516255860282270.0139725247656327



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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