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Coexpression cluster:C1259: Difference between revisions

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

Latest revision as of 11:41, 17 September 2013


Full id: C1259_Neurons_parietal_occipital_temporal_brain_duodenum_glioblastoma



Phase1 CAGE Peaks

Hg19::chr20:62009349..62009358,-p10@CHRNA4
Hg19::chr2:104423528..104423529,-p@chr2:104423528..104423529
-
Hg19::chr4:176734316..176734327,-p25@GPM6A
Hg19::chr4:176734368..176734405,-p19@GPM6A
Hg19::chr9:100199546..100199572,-p@chr9:100199546..100199572
-
Hg19::chr9:100199913..100199937,-p@chr9:100199913..100199937
-
Hg19::chr9:100199938..100199951,-p@chr9:100199938..100199951
-


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

GO IDGO nameFDR corrected p-value
GO:0035094response to nicotine0.0116780462456223
GO:0043279response to alkaloid0.0116780462456223
GO:0014070response to organic cyclic substance0.0116780462456223
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0116780462456223
GO:0015464acetylcholine receptor activity0.0116780462456223
GO:0042166acetylcholine binding0.0116780462456223
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0116780462456223
GO:0005887integral to plasma membrane0.0116780462456223
GO:0031226intrinsic to plasma membrane0.0116780462456223
GO:0043176amine binding0.0172001288703765
GO:0001666response to hypoxia0.0172001288703765
GO:0010033response to organic substance0.0203612309968446
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0216421112045033
GO:0044459plasma membrane part0.0216421112045033
GO:0043235receptor complex0.0280579879925454
GO:0005230extracellular ligand-gated ion channel activity0.0280579879925454
GO:0030594neurotransmitter receptor activity0.0280579879925454
GO:0042165neurotransmitter binding0.0280579879925454
GO:0009986cell surface0.0280579879925454
GO:0045211postsynaptic membrane0.0280579879925454
GO:0044456synapse part0.0280579879925454
GO:0015276ligand-gated ion channel activity0.0280579879925454
GO:0022834ligand-gated channel activity0.0280579879925454
GO:0005886plasma membrane0.0352157565233113
GO:0007268synaptic transmission0.0455607017688047
GO:0019226transmission of nerve impulse0.0498214260109094



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><br>

Cell Type
Ontology termp-valuen
neuron4.90e-386
neuroblast4.90e-386
electrically signaling cell4.90e-386
neuronal stem cell9.31e-298
neural cell4.87e-0925
Uber Anatomy
Ontology termp-valuen
central nervous system1.14e-1481
nervous system3.06e-1389
neocortex2.90e-1120
regional part of cerebral cortex2.41e-1022
duodenum1.67e-092
cerebral cortex3.16e-0925
pallium3.16e-0925
regional part of telencephalon2.12e-0732
cerebral hemisphere2.12e-0732
brain grey matter5.19e-0734
gray matter5.19e-0734
telencephalon5.19e-0734
ectoderm-derived structure5.71e-07171
ectoderm5.71e-07171
presumptive ectoderm5.71e-07171
organ system subdivision6.23e-07223


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.12.03099
MA0031.10.809638
MA0038.10.60704
MA0040.13.41227
MA0041.10.521615
MA0042.11.22641
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.11.39306
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.13.21622
MA0092.12.05178
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.11.36091
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.12.46913
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.000432051
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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

No analysis results for this cluster

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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