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Coexpression cluster:C837: Difference between revisions

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}}
}}

Revision as of 19:29, 22 January 2013


Full id: C837_neuroectodermal_duodenum_temporal_occipital_medial_carcinoid_parietal



Phase1 CAGE Peaks

Hg19::chr15:77907249..77907288,-p9@LINGO1
Hg19::chr15:77907545..77907560,-p4@LINGO1
Hg19::chr15:77907829..77907849,-p11@LINGO1
Hg19::chr15:77907867..77907879,-p12@LINGO1
Hg19::chr15:77907974..77907985,-p8@LINGO1
Hg19::chr15:77908039..77908050,-p14@LINGO1
Hg19::chr15:78111788..78111799,-p@chr15:78111788..78111799
-
Hg19::chr3:51741072..51741106,+p1@GRM2
Hg19::chr6:110422944..110422955,-p7@AK056044
Hg19::chr8:50823900..50823915,+p6@SNTG1


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:0014047glutamate secretion0.00759426602163143
GO:0016013syntrophin complex0.00759426602163143
GO:0042734presynaptic membrane0.0189784004164746
GO:0031280negative regulation of cyclase activity0.0189784004164746
GO:0007194negative regulation of adenylate cyclase activity0.0189784004164746
GO:0051350negative regulation of lyase activity0.0189784004164746
GO:0016010dystrophin-associated glycoprotein complex0.0238536438879483
GO:0030424axon0.0245064420408919
GO:0005605basal lamina0.0245064420408919
GO:0007269neurotransmitter secretion0.0245064420408919
GO:0045761regulation of adenylate cyclase activity0.0245064420408919
GO:0031279regulation of cyclase activity0.0245064420408919
GO:0051339regulation of lyase activity0.0245064420408919
GO:0045055regulated secretory pathway0.0287065807247769
GO:0008067metabotropic glutamate, GABA-B-like receptor activity0.0288115129303549
GO:0003001generation of a signal involved in cell-cell signaling0.029956787610063
GO:0005604basement membrane0.029956787610063
GO:0001505regulation of neurotransmitter levels0.029956787610063
GO:0043005neuron projection0.029956787610063
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.029956787610063
GO:0043086negative regulation of catalytic activity0.029956787610063
GO:0019933cAMP-mediated signaling0.029956787610063
GO:0008066glutamate receptor activity0.0309534539371326
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0368968572996878
GO:0019935cyclic-nucleotide-mediated signaling0.0369292580465969
GO:0044420extracellular matrix part0.0381182985017164
GO:0044459plasma membrane part0.0412763404122513
GO:0044456synapse part0.0434629625940273



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
neuron4.26e-136
neuroblast4.26e-136
electrically signaling cell4.26e-136
embryonic stem cell2.44e-115
neuronal stem cell1.27e-098
Uber Anatomy
Ontology termp-valuen
central nervous system2.68e-6781
neural tube5.46e-6456
neural rod5.46e-6456
future spinal cord5.46e-6456
neural keel5.46e-6456
nervous system9.60e-6289
regional part of nervous system1.00e-6153
regional part of brain1.00e-6153
telencephalon1.05e-5434
brain grey matter2.18e-5434
gray matter2.18e-5434
regional part of forebrain1.09e-5341
forebrain1.09e-5341
anterior neural tube1.09e-5341
future forebrain1.09e-5341
brain8.82e-5368
future brain8.82e-5368
cerebral hemisphere3.31e-5132
regional part of telencephalon7.97e-5132
neurectoderm8.11e-4986
regional part of cerebral cortex1.00e-4722
neocortex2.00e-4320
neural plate7.38e-4282
presumptive neural plate7.38e-4282
cerebral cortex2.15e-4125
pallium2.15e-4125
pre-chordal neural plate4.33e-3561
ectoderm-derived structure1.39e-33171
ectoderm1.39e-33171
presumptive ectoderm1.39e-33171
ecto-epithelium5.26e-32104
adult organism5.27e-31114
structure with developmental contribution from neural crest6.56e-24132
organ system subdivision9.17e-22223
basal ganglion4.43e-159
nuclear complex of neuraxis4.43e-159
aggregate regional part of brain4.43e-159
collection of basal ganglia4.43e-159
cerebral subcortex4.43e-159
gyrus7.53e-156
neural nucleus3.59e-149
nucleus of brain3.59e-149
temporal lobe5.88e-136
occipital lobe1.23e-125
parietal lobe1.42e-125
limbic system2.11e-125
tube7.44e-12192
posterior neural tube1.01e-1115
chordal neural plate1.01e-1115
telencephalic nucleus8.89e-117
segmental subdivision of hindbrain1.35e-0912
hindbrain1.35e-0912
presumptive hindbrain1.35e-0912
segmental subdivision of nervous system9.38e-0913
anatomical cluster1.45e-08373
frontal cortex3.26e-083
brainstem4.07e-086
regional part of metencephalon1.02e-079
metencephalon1.02e-079
future metencephalon1.02e-079
anatomical conduit2.52e-07240
organ part9.53e-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)
MA0003.11.34002
MA0004.10.380329
MA0006.11.23783
MA0007.10.952442
MA0009.10.828613
MA0014.11.9973
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
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
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.12.04431
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.11.12112
MA0072.10.798564
MA0073.10.431725
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.55119
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.12.12878
MA0101.10.241637
MA0103.11.20737
MA0105.11.13797
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.11.35344
MA0146.10.606611
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.360905
MA0138.21.39695
MA0002.20.129981
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.20.573053
MA0065.20.0371828
MA0150.11.52802
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.990939
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.300798
MA0102.21.36707
MA0258.10.919347
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

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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