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Coexpression cluster:C4279: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4279_skeletal_diaphragm_heart_tongue_left_penis_throat
|gostat_on_coexpression_clusters=GO:0017025!TATA-binding protein binding!0.00777099123786688!23066$GO:0005844!polysome!0.0174829288234617!7957$GO:0005977!glycogen metabolic process!0.0370821653336492!7957$GO:0006073!glucan metabolic process!0.0370821653336492!7957$GO:0006112!energy reserve metabolic process!0.0370821653336492!7957$GO:0008138!protein tyrosine/serine/threonine phosphatase activity!0.0370821653336492!7957$GO:0043687!post-translational protein modification!0.0370821653336492!7957;23066$GO:0044264!cellular polysaccharide metabolic process!0.0370821653336492!7957$GO:0005976!polysaccharide metabolic process!0.0370821653336492!7957$GO:0006464!protein modification process!0.0378194588250887!7957;23066$GO:0043412!biopolymer modification!0.0378194588250887!7957;23066$GO:0015980!energy derivation by oxidation of organic compounds!0.0378194588250887!7957
|id=C4279
}}

Latest revision as of 12:42, 17 September 2013


Full id: C4279_skeletal_diaphragm_heart_tongue_left_penis_throat



Phase1 CAGE Peaks

Hg19::chr3:12838161..12838215,+p1@CAND2
Hg19::chr6:146056648..146056679,-p2@EPM2A
Hg19::chr6:146056691..146056735,-p3@EPM2A


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:0017025TATA-binding protein binding0.00777099123786688
GO:0005844polysome0.0174829288234617
GO:0005977glycogen metabolic process0.0370821653336492
GO:0006073glucan metabolic process0.0370821653336492
GO:0006112energy reserve metabolic process0.0370821653336492
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0370821653336492
GO:0043687post-translational protein modification0.0370821653336492
GO:0044264cellular polysaccharide metabolic process0.0370821653336492
GO:0005976polysaccharide metabolic process0.0370821653336492
GO:0006464protein modification process0.0378194588250887
GO:0043412biopolymer modification0.0378194588250887
GO:0015980energy derivation by oxidation of organic compounds0.0378194588250887



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 organism1.53e-42114
nervous system4.68e-3089
central nervous system2.75e-2981
neural tube1.11e-2656
neural rod1.11e-2656
future spinal cord1.11e-2656
neural keel1.11e-2656
brain5.31e-2568
future brain5.31e-2568
regional part of nervous system6.73e-2553
regional part of brain6.73e-2553
regional part of forebrain3.41e-2241
forebrain3.41e-2241
anterior neural tube3.41e-2241
future forebrain3.41e-2241
ectoderm-derived structure5.37e-21171
ectoderm5.37e-21171
presumptive ectoderm5.37e-21171
neurectoderm5.48e-2086
neural plate1.10e-1982
presumptive neural plate1.10e-1982
brain grey matter1.24e-1834
gray matter1.24e-1834
telencephalon1.37e-1834
cerebral hemisphere2.05e-1732
regional part of telencephalon2.11e-1732
organ system subdivision1.06e-16223
pre-chordal neural plate1.01e-1561
ecto-epithelium4.32e-15104
structure with developmental contribution from neural crest6.40e-14132
cerebral cortex1.77e-1325
pallium1.77e-1325
regional part of cerebral cortex9.12e-1322
neocortex9.62e-1220
organ1.09e-08503
multi-cellular organism1.64e-08656
anatomical cluster2.97e-08373
germ layer3.93e-07560
germ layer / neural crest3.93e-07560
embryonic tissue3.93e-07560
presumptive structure3.93e-07560
germ layer / neural crest derived structure3.93e-07560
epiblast (generic)3.93e-07560
anatomical group8.88e-07625


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)
MA0003.13.22681
MA0004.11.93041
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.12.854
MA0060.11.23283
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
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
BCLAF1#9774214.43509840674790.006201147435546130.0273925321245613
CCNT2#90536.336201576962630.003930750035764890.0190577783290121
E2F4#1874312.66806031528440.0004917987006298980.00438026304750861
E2F6#187635.017155731697390.00791769806886330.032335528432879
ELF1#199734.258097958807540.01295179875054610.0463720572405994
GTF2B#2959331.94382993432423.06634405746243e-050.000628796204628547
HMGN3#932438.178547723350590.001827766942164210.0108943129592905
JUNB#3726220.40708843988080.003131462199438740.0164518728631814
SETDB1#9869226.8800174520070.001814468907964410.010896516490075
TFAP2A#7020211.01242291536330.01054990655215560.0390287871630684
YY1#752834.911170749853860.008441455341808260.0330366916901414



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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