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Coexpression cluster:C1799: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:52, 17 September 2013


Full id: C1799_occipital_duodenum_temporal_Wilms_brain_pineal_parietal



Phase1 CAGE Peaks

Hg19::chr18:43913919..43913967,+p2@RNF165
Hg19::chr18:43913973..43914005,+p1@RNF165
Hg19::chr18:43914019..43914036,+p4@RNF165
Hg19::chr18:43914051..43914066,+p5@RNF165
Hg19::chr18:43914159..43914222,+p3@RNF165


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
nervous system1.29e-3489
central nervous system4.53e-3481
regional part of nervous system4.51e-3153
regional part of brain4.51e-3153
brain6.03e-3068
future brain6.03e-3068
neural tube7.20e-3056
neural rod7.20e-3056
future spinal cord7.20e-3056
neural keel7.20e-3056
regional part of forebrain2.91e-2741
forebrain2.91e-2741
anterior neural tube2.91e-2741
future forebrain2.91e-2741
adult organism4.98e-27114
organ system subdivision1.65e-26223
telencephalon6.71e-2434
neural plate8.42e-2482
presumptive neural plate8.42e-2482
neurectoderm1.73e-2386
brain grey matter2.13e-2334
gray matter2.13e-2334
cerebral hemisphere2.19e-2332
regional part of telencephalon1.40e-2232
ectoderm-derived structure4.49e-21171
ectoderm4.49e-21171
presumptive ectoderm4.49e-21171
pre-chordal neural plate1.20e-1961
cerebral cortex9.26e-1925
pallium9.26e-1925
ecto-epithelium1.39e-18104
regional part of cerebral cortex1.84e-1822
neocortex6.34e-1720
structure with developmental contribution from neural crest4.15e-13132
anatomical cluster8.69e-11373
organ part2.25e-10218
multi-tissue structure6.14e-08342
embryo2.17e-07592
basal ganglion9.11e-079
nuclear complex of neuraxis9.11e-079
aggregate regional part of brain9.11e-079
collection of basal ganglia9.11e-079
cerebral subcortex9.11e-079


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)
MA0003.14.3611
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.19.98148
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.12.41212
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.13.37159
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.10.522232
MA0060.17.51067
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.92967
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.10.946108
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.21.41923
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.22.73531
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.16.5409
MA0163.12.54221
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.25.25626
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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
E2F1#186954.907389214879320.0003512818099256460.0035279854742595
E2F6#187644.013724585357910.006632118233933880.0282969113585187
REST#597835.790017229676810.009468788694433940.0357007517132847
TCF7L2#6934510.77017656313736.89693748574565e-060.000199808392253478



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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