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{{Coexpression_clusters
{
|full_id=C317_Neutrophils_medial_amygdala_occipital_hippocampus_brain_parietal
 

Latest revision as of 11:20, 17 September 2013


Full id: C317_Neutrophils_medial_amygdala_occipital_hippocampus_brain_parietal



Phase1 CAGE Peaks

Hg19::chr10:12872736..12872766,+p@chr10:12872736..12872766
+
Hg19::chr10:28872321..28872338,+p@chr10:28872321..28872338
+
Hg19::chr17:8063613..8063632,-p19@VAMP2
Hg19::chr17:8063633..8063652,-p13@VAMP2
Hg19::chr17:8063773..8063784,-p17@VAMP2
Hg19::chr17:8063896..8063935,-p5@VAMP2
Hg19::chr17:8063940..8064027,-p3@VAMP2
Hg19::chr17:8064030..8064075,-p4@VAMP2
Hg19::chr17:8064076..8064105,-p7@VAMP2
Hg19::chr17:8064108..8064167,-p2@VAMP2
Hg19::chr17:8064820..8064846,-p@chr17:8064820..8064846
-
Hg19::chr17:8064981..8064994,-p@chr17:8064981..8064994
-
Hg19::chr17:8065006..8065022,-p@chr17:8065006..8065022
-
Hg19::chr17:8065032..8065092,-p@chr17:8065032..8065092
-
Hg19::chr17:8065618..8065647,-p6@VAMP2
Hg19::chr19:21476394..21476407,-p5@ZNF708
Hg19::chr1:182352898..182352944,-p@chr1:182352898..182352944
-
Hg19::chr22:22162032..22162049,-p@chr22:22162032..22162049
-
Hg19::chr22:22221658..22221669,-p2@MAPK1
Hg19::chr2:55252842..55252854,-p37@RTN4
Hg19::chr2:55253582..55253618,-p21@RTN4
Hg19::chr4:146296807..146296819,+p2@RTN3P1
Hg19::chr5:108714170..108714199,-p@chr5:108714170..108714199
-
Hg19::chr5:108714529..108714568,-p@chr5:108714529..108714568
-
Hg19::chr5:108717346..108717361,-p@chr5:108717346..108717361
-
Hg19::chr7:135614485..135614494,-p@chr7:135614485..135614494
-
Hg19::chrX:148561290..148561301,-p@chrX:148561290..148561301
-
Hg19::chrX:148561796..148561820,-p7@IDS
Hg19::chrX:148562594..148562662,-p9@IDS
Hg19::chrX:148562710..148562819,-p5@IDS
Hg19::chrX:148563677..148563702,-p15@IDS
Hg19::chrX:148564109..148564137,-p@chrX:148564109..148564137
-
Hg19::chrX:148564140..148564173,-p@chrX:148564140..148564173
-
Hg19::chrX:148564210..148564228,-p@chrX:148564210..148564228
-
Hg19::chrX:148568487..148568517,-p@chrX:148568487..148568517
-
Hg19::chrX:148579666..148579690,-p12@IDS
Hg19::chrX:17095433..17095443,+p@chrX:17095433..17095443
+


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:0051093negative regulation of developmental process0.011056054917044
GO:0004423iduronate-2-sulfatase activity0.0148286915920051
GO:0019858cytosine metabolic process0.0148286915920051
GO:0019987negative regulation of anti-apoptosis0.0148286915920051
GO:0043330response to exogenous dsRNA0.0148286915920051
GO:0030517negative regulation of axon extension0.0148286915920051
GO:0050793regulation of developmental process0.0148286915920051
GO:0032496response to lipopolysaccharide0.014872125970684
GO:0031663lipopolysaccharide-mediated signaling pathway0.014872125970684
GO:0001784phosphotyrosine binding0.014872125970684
GO:0045309protein phosphorylated amino acid binding0.014872125970684
GO:0043331response to dsRNA0.014872125970684
GO:0050771negative regulation of axonogenesis0.014872125970684
GO:0002237response to molecule of bacterial origin0.0214743725119483
GO:0051219phosphoprotein binding0.0214743725119483
GO:0050768negative regulation of neurogenesis0.0214743725119483
GO:0045767regulation of anti-apoptosis0.0214743725119483
GO:0030516regulation of axon extension0.0214743725119483
GO:0006206pyrimidine base metabolic process0.0220381900309618
GO:0048675axon extension0.027371766138232
GO:0042981regulation of apoptosis0.0276148747912329
GO:0043067regulation of programmed cell death0.0276148747912329
GO:0043229intracellular organelle0.0291760839094347
GO:0043226organelle0.0291760839094347
GO:0009112nucleobase metabolic process0.0296154479966804
GO:0050770regulation of axonogenesis0.0321850191184355
GO:0008484sulfuric ester hydrolase activity0.0381317353245734
GO:0004707MAP kinase activity0.0390634055895234
GO:0019717synaptosome0.0399303007690236
GO:0050767regulation of neurogenesis0.0407388984608223
GO:0006915apoptosis0.0418259096100216
GO:0012501programmed cell death0.0418259096100216
GO:0008219cell death0.0435619786122206
GO:0016265death0.0435619786122206
GO:0030203glycosaminoglycan metabolic process0.0446382964742239
GO:0006022aminoglycan metabolic process0.0446382964742239
GO:0030176integral to endoplasmic reticulum membrane0.0460296366314013
GO:0044424intracellular part0.0465090500924841
GO:0030334regulation of cell migration0.0477864562370677
GO:0009653anatomical structure morphogenesis0.0477864562370677
GO:0031227intrinsic to endoplasmic reticulum membrane0.0477864562370677
GO:0045596negative regulation of cell differentiation0.0493315820358417
GO:0005737cytoplasm0.0493315820358417
GO:0051270regulation of cell motility0.0498513608352335
GO:0048523negative regulation of cellular process0.0498513608352335
GO:0040012regulation of locomotion0.0498513608352335
GO:0040011locomotion0.0498513608352335



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
neural tube2.95e-3456
neural rod2.95e-3456
future spinal cord2.95e-3456
neural keel2.95e-3456
central nervous system1.18e-3381
adult organism3.77e-33114
nervous system3.65e-3289
regional part of nervous system5.18e-3253
regional part of brain5.18e-3253
brain3.89e-3068
future brain3.89e-3068
regional part of forebrain2.65e-2841
forebrain2.65e-2841
anterior neural tube2.65e-2841
future forebrain2.65e-2841
neurectoderm8.21e-2486
brain grey matter9.64e-2434
gray matter9.64e-2434
telencephalon1.61e-2334
neural plate2.36e-2382
presumptive neural plate2.36e-2382
cerebral hemisphere2.72e-2232
regional part of telencephalon3.05e-2232
regional part of cerebral cortex6.94e-1822
pre-chordal neural plate2.73e-1761
cerebral cortex5.18e-1725
pallium5.18e-1725
neocortex3.46e-1620
ectoderm-derived structure2.05e-14171
ectoderm2.05e-14171
presumptive ectoderm2.05e-14171
ecto-epithelium6.62e-14104
structure with developmental contribution from neural crest7.12e-14132
organ system subdivision2.18e-12223
basal ganglion1.84e-089
nuclear complex of neuraxis1.84e-089
aggregate regional part of brain1.84e-089
collection of basal ganglia1.84e-089
cerebral subcortex1.84e-089
neural nucleus3.16e-089
nucleus of brain3.16e-089
posterior neural tube2.42e-0715
chordal neural plate2.42e-0715
telencephalic nucleus9.25e-077


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)
MA0003.11.01724e-06
MA0004.10.227494
MA0006.10.017801
MA0007.10.454587
MA0009.10.348676
MA0014.10.0758233
MA0017.10.109976
MA0019.10.133515
MA0024.10.269509
MA0025.10.457382
MA0027.11.8693
MA0028.10.437351
MA0029.10.774607
MA0030.10.275218
MA0031.10.229546
MA0038.10.354223
MA0040.10.28793
MA0041.10.0709832
MA0042.11.22701
MA0043.10.348924
MA0046.10.340164
MA0048.10.00204631
MA0050.10.0588428
MA0051.10.708538
MA0052.10.290795
MA0055.10.087434
MA0056.10
MA0057.10.0232245
MA0058.10.131305
MA0059.10.0320159
MA0060.10.00361847
MA0061.10.110661
MA0063.10
MA0066.10.354793
MA0067.10.617744
MA0068.10.236871
MA0069.10.895136
MA0070.10.328499
MA0071.10.303897
MA0072.10.325036
MA0073.14.79849e-13
MA0074.10.107076
MA0076.10.33811
MA0077.10.319123
MA0078.10.162277
MA0081.10.563288
MA0083.10.354583
MA0084.10.789341
MA0087.10.323157
MA0088.10.00482556
MA0089.10
MA0090.10.364676
MA0091.11.80101
MA0092.10.0507443
MA0093.10.0826495
MA0095.10
MA0098.10
MA0100.10.116712
MA0101.10.0190019
MA0103.10.926271
MA0105.10.245845
MA0106.10.131372
MA0107.10.00792473
MA0108.20.227449
MA0109.10
MA0111.10.390215
MA0113.10.140523
MA0114.10.234565
MA0115.10.549953
MA0116.10.00831185
MA0117.10.37852
MA0119.10.11642
MA0122.10.399455
MA0124.10.513817
MA0125.11.12571
MA0130.10
MA0131.10.173329
MA0132.10
MA0133.10
MA0135.11.7306
MA0136.10.113182
MA0139.10.0110859
MA0140.10.300545
MA0141.10.883016
MA0142.10.208133
MA0143.10.140623
MA0144.10.206726
MA0145.10.0071176
MA0146.10.0173439
MA0147.10.125089
MA0148.10.073613
MA0149.12.69095
MA0062.20.0428221
MA0035.20.299658
MA0039.20.00021536
MA0138.20.949565
MA0002.20.414963
MA0137.20.0968741
MA0104.20.150849
MA0047.20.393809
MA0112.20.00572278
MA0065.20.489181
MA0150.10.0392652
MA0151.10
MA0152.12.15672
MA0153.10.42835
MA0154.10.0392757
MA0155.10.000223711
MA0156.10.459853
MA0157.10.190314
MA0158.10
MA0159.10.451444
MA0160.10.975924
MA0161.10
MA0162.10.00285002
MA0163.10.000233058
MA0164.10.451884
MA0080.20.0827099
MA0018.20.132133
MA0099.20.309305
MA0079.27.46717e-06
MA0102.20.824164
MA0258.10.00516272
MA0259.10.00973533
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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