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Coexpression cluster:C778: Difference between revisions

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{{Coexpression_clusters
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|full_id=C778_thalamus_substantia_optic_spinal_globus_hippocampus_corpus
|id=C778
}}

Latest revision as of 11:30, 17 September 2013


Full id: C778_thalamus_substantia_optic_spinal_globus_hippocampus_corpus



Phase1 CAGE Peaks

Hg19::chr10:104846929..104846933,+p@chr10:104846929..104846933
+
Hg19::chr14:45603433..45603463,-p@chr14:45603433..45603463
-
Hg19::chr16:15489814..15489859,+p2@MPV17L
Hg19::chr19:36705547..36705597,-p1@ZNF565
Hg19::chr19:53636125..53636178,-p1@ZNF415
Hg19::chr1:92545866..92545917,+p1@BTBD8
Hg19::chr2:230786032..230786119,-p4@TRIP12
Hg19::chr2:3522634..3522680,-p@chr2:3522634..3522680
-
Hg19::chr3:37217852..37217899,+p@chr3:37217852..37217899
+
Hg19::chr8:102195406..102195412,-p1@BC035156


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 organism1.66e-45114
nervous system9.54e-3189
neural tube2.62e-3056
neural rod2.62e-3056
future spinal cord2.62e-3056
neural keel2.62e-3056
central nervous system2.83e-3081
regional part of nervous system2.53e-2853
regional part of brain2.53e-2853
brain2.59e-2768
future brain2.59e-2768
regional part of forebrain1.26e-2541
forebrain1.26e-2541
anterior neural tube1.26e-2541
future forebrain1.26e-2541
neurectoderm3.98e-2486
neural plate1.26e-2282
presumptive neural plate1.26e-2282
brain grey matter2.37e-2134
gray matter2.37e-2134
telencephalon3.09e-2134
ectoderm-derived structure5.79e-21171
ectoderm5.79e-21171
presumptive ectoderm5.79e-21171
regional part of telencephalon5.15e-2032
cerebral hemisphere6.55e-2032
pre-chordal neural plate7.25e-1861
organ system subdivision6.59e-17223
cerebral cortex1.26e-1525
pallium1.26e-1525
ecto-epithelium2.14e-15104
regional part of cerebral cortex3.36e-1522
structure with developmental contribution from neural crest6.30e-14132
neocortex6.60e-1420
neural nucleus3.34e-079
nucleus of brain3.34e-079
basal ganglion4.51e-079
nuclear complex of neuraxis4.51e-079
aggregate regional part of brain4.51e-079
collection of basal ganglia4.51e-079
cerebral subcortex4.51e-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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.665232
MA0007.10.952442
MA0009.10.828613
MA0014.10.15363
MA0017.10.270554
MA0019.11.29263
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.14.59581
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.12.31263
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0214747
MA0074.10.4723
MA0076.14.11822
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.189717
MA0106.11.28468
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.02702
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.11.43152
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.332712
MA0146.11.8264
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.23.8434
MA0035.20.437071
MA0039.20.713007
MA0138.20.569505
MA0002.20.407187
MA0137.20.710884
MA0104.20.845907
MA0047.20.504873
MA0112.20.904106
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.12484
MA0156.11.31919
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.229496
MA0163.10.990939
MA0164.11.34364
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.166297
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
CHD2#110644.137609133646740.01136509692198320.0416608528108877
GABPB1#255353.533841918091090.007669373268468170.0315856963912436
HEY1#2346272.8280777301740.003295391007019310.0170472703641631
IRF1#365953.818581876781950.005465628575453730.0247560405408887
NRF1#489944.884111779084360.00630934732180550.0278257643233835
TAF1#687282.674437028596230.001556617278062390.00988397081125715



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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