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{{Coexpression_clusters
{
|full_id=C2970_optic_corpus_spinal_thalamus_thyroid_diencephalon_globus
|

Latest revision as of 12:16, 17 September 2013


Full id: C2970_optic_corpus_spinal_thalamus_thyroid_diencephalon_globus



Phase1 CAGE Peaks

Hg19::chr10:102133271..102133305,+p4@LINC00263
Hg19::chr4:42659057..42659100,-p2@ATP8A1
Hg19::chr4:42659102..42659161,-p1@ATP8A1


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:0015917aminophospholipid transport0.00476863299187566
GO:0004012phospholipid-translocating ATPase activity0.00874249381843871
GO:0015247aminophospholipid transporter activity0.00874249381843871
GO:0015914phospholipid transport0.00874249381843871
GO:0005548phospholipid transporter activity0.0101730837160014
GO:0019829cation-transporting ATPase activity0.0217994651057173
GO:0005319lipid transporter activity0.0217994651057173
GO:0006869lipid transport0.0256093253267397
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0256093253267397
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0321087954786294
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0321087954786294
GO:0043492ATPase activity, coupled to movement of substances0.0321087954786294
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0321087954786294
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0321087954786294
GO:0015399primary active transmembrane transporter activity0.0321087954786294
GO:0031410cytoplasmic vesicle0.0394736842105263
GO:0031982vesicle0.0394736842105263
GO:0000287magnesium ion binding0.0394736842105263
GO:0042623ATPase activity, coupled0.0441726003457956
GO:0016887ATPase activity0.0499911691981632



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>

Uber Anatomy
Ontology termp-valuen
adult organism2.97e-41114
neural tube1.60e-2556
neural rod1.60e-2556
future spinal cord1.60e-2556
neural keel1.60e-2556
regional part of nervous system7.15e-2453
regional part of brain7.15e-2453
central nervous system1.79e-2181
regional part of forebrain2.10e-2141
forebrain2.10e-2141
anterior neural tube2.10e-2141
future forebrain2.10e-2141
nervous system8.67e-2089
brain2.83e-1968
future brain2.83e-1968
neural plate5.39e-1882
presumptive neural plate5.39e-1882
telencephalon5.89e-1834
brain grey matter8.34e-1834
gray matter8.34e-1834
regional part of telencephalon1.05e-1632
cerebral hemisphere1.37e-1632
neurectoderm1.67e-1686
pre-chordal neural plate1.53e-1461
regional part of cerebral cortex4.28e-1322
cerebral cortex1.35e-1225
pallium1.35e-1225
neocortex4.58e-1220
ecto-epithelium4.60e-10104
hemolymphoid system5.52e-09108
hematopoietic system5.67e-0998
blood island5.67e-0998
organ system subdivision1.37e-07223
structure with developmental contribution from neural crest1.75e-07132
neural nucleus9.18e-079
nucleus of brain9.18e-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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.12.25834
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.776149
MA0164.12.32251
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.72079
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BRCA1#672213.45615376214920.007119807716084560.02960605184186
CCNT2#90536.336201576962630.003930750035764890.0188998482107292
E2F1#186934.907389214879320.008460985347239390.0323269379433084
EBF1#187938.9064668465690.00141523283560980.00912323326450542
EGR1#195834.988179094810140.008056488137383440.0318825192141332
ELF1#199734.258097958807540.01295179875054610.0459686301131069
EP300#203336.77394172622320.003216880500103790.016674166586448
FOXA1#3169311.08141974938550.000734755275698670.00579191684192719
IRF1#365937.63716375356390.002244692747297240.0127527316452688
SIX5#147912211.3911435703060.009873820081429030.037053966779891
SP1#666735.69838137814090.005403962701712170.0245277905521129
SREBF2#67211145.6477541371160.006850215514569990.0290423665716561
USF1#739136.361499277207960.00388404057290560.0189385738546939
ZBTB7A#5134137.35190930787590.002516255860282270.0139539768381044
ZNF263#1012738.221841637010680.001799043925565870.0108865141979358



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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