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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:45, 17 September 2013


Full id: C4439_ductus_seminal_pons_mesothelioma_medulla_rectal_brain



Phase1 CAGE Peaks

Hg19::chr4:89079686..89079698,-p9@ABCG2
Hg19::chr4:89079714..89079746,-p4@ABCG2
Hg19::chr4:89079757..89079802,-p2@ABCG2


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism7.26e-51114
neural tube2.94e-4056
neural rod2.94e-4056
future spinal cord2.94e-4056
neural keel2.94e-4056
regional part of nervous system3.26e-3753
regional part of brain3.26e-3753
regional part of forebrain2.48e-3341
forebrain2.48e-3341
anterior neural tube2.48e-3341
future forebrain2.48e-3341
central nervous system1.48e-3081
brain2.30e-3068
future brain2.30e-3068
telencephalon1.32e-2634
brain grey matter2.19e-2634
gray matter2.19e-2634
nervous system1.78e-2589
neural plate7.38e-2582
presumptive neural plate7.38e-2582
cerebral hemisphere1.96e-2432
regional part of telencephalon2.24e-2432
neurectoderm8.04e-2386
regional part of cerebral cortex1.72e-2122
pre-chordal neural plate3.54e-2161
neocortex9.88e-2020
organ system subdivision2.83e-19223
cerebral cortex5.21e-1825
pallium5.21e-1825
ecto-epithelium2.45e-17104
structure with developmental contribution from neural crest2.08e-15132
anatomical cluster2.50e-13373
anatomical conduit4.43e-13240
tube3.45e-12192
neural nucleus5.37e-109
nucleus of brain5.37e-109
ectoderm-derived structure6.77e-10171
ectoderm6.77e-10171
presumptive ectoderm6.77e-10171
basal ganglion8.02e-109
nuclear complex of neuraxis8.02e-109
aggregate regional part of brain8.02e-109
collection of basal ganglia8.02e-109
cerebral subcortex8.02e-109
organ1.02e-09503
multi-tissue structure3.11e-09342
posterior neural tube2.66e-0815
chordal neural plate2.66e-0815
diencephalon3.53e-087
future diencephalon3.53e-087
telencephalic nucleus5.45e-087
brainstem5.72e-086
gyrus1.05e-076
organ part2.97e-07218


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
MA0006.11.5435
MA0007.13.13838
MA0009.11.3275
MA0014.10.758317
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
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
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
CCNT2#90536.336201576962630.003930750035764890.0190790353202235
E2F1#186934.907389214879320.008460985347239390.0326977557328523
EGR1#195834.988179094810140.008056488137383440.0321960497658295
FOS#235338.99795530889440.001372499272417130.00900731755133672
FOSL2#2355316.93020060456170.0002060162053171620.00243864065137924
GATA1#2623313.56030814380040.0004009615963782630.00389001655031579
JUN#3725312.51282919233630.0005103313992726250.0044578873376241
JUND#372736.994663941871030.002921845042734990.0157385411531384
TAL1#6886219.91241111829350.003287176608740550.017019107566937



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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