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Coexpression cluster:C2996

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Full id: C2996_optic_CD4_corpus_thalamus_globus_spinal_diencephalon



Phase1 CAGE Peaks

Hg19::chr10:14613932..14613943,-p9@FAM107B
Hg19::chr10:14613968..14614048,-p2@FAM107B
Hg19::chr5:80256453..80256506,+p2@RASGRF2


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:0005089Rho guanyl-nucleotide exchange factor activity0.0470387377840574
GO:0035023regulation of Rho protein signal transduction0.0470387377840574
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0470387377840574
GO:0007266Rho protein signal transduction0.0470387377840574



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
mature alpha-beta T cell1.92e-2018
alpha-beta T cell1.92e-2018
immature T cell1.92e-2018
mature T cell1.92e-2018
immature alpha-beta T cell1.92e-2018
CD8-positive, alpha-beta T cell6.12e-1511
T cell5.20e-1325
pro-T cell5.20e-1325
CD4-positive, alpha-beta T cell1.06e-086
Uber Anatomy
Ontology termp-valuen
adult organism2.97e-60114
neural tube1.66e-3656
neural rod1.66e-3656
future spinal cord1.66e-3656
neural keel1.66e-3656
regional part of nervous system4.18e-3353
regional part of brain4.18e-3353
regional part of forebrain8.76e-2741
forebrain8.76e-2741
anterior neural tube8.76e-2741
future forebrain8.76e-2741
brain2.40e-2668
future brain2.40e-2668
central nervous system3.05e-2681
telencephalon1.12e-2534
brain grey matter2.74e-2534
gray matter2.74e-2534
nervous system2.22e-2389
cerebral hemisphere2.47e-2332
regional part of telencephalon3.38e-2332
neural plate1.99e-2282
presumptive neural plate1.99e-2282
neurectoderm1.17e-2086
regional part of cerebral cortex7.32e-1922
neocortex7.35e-1720
cerebral cortex6.93e-1625
pallium6.93e-1625
pre-chordal neural plate9.34e-1661
ecto-epithelium1.71e-14104
organ system subdivision3.87e-12223
neural nucleus1.89e-119
nucleus of brain1.89e-119
basal ganglion2.97e-119
nuclear complex of neuraxis2.97e-119
aggregate regional part of brain2.97e-119
collection of basal ganglia2.97e-119
cerebral subcortex2.97e-119
structure with developmental contribution from neural crest6.84e-11132
posterior neural tube1.05e-1015
chordal neural plate1.05e-1015
blood7.21e-1015
haemolymphatic fluid7.21e-1015
organism substance7.21e-1015
telencephalic nucleus2.53e-097
segmental subdivision of nervous system1.06e-0813
brainstem1.45e-086
gyrus4.95e-086
tube9.39e-08192
segmental subdivision of hindbrain1.60e-0712
hindbrain1.60e-0712
presumptive hindbrain1.60e-0712
ectoderm-derived structure4.08e-07171
ectoderm4.08e-07171
presumptive ectoderm4.08e-07171
limbic system9.97e-075


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
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
MA0073.10.668628
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
MA0105.10.31555
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
MA0143.12.29531
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
MA0112.20.264678
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
MA0162.10.149099
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
BHLHE40#8553229.91454236465160.001467483527106140.00939338760035785
ESR1#2099220.51240219743630.003099741577095180.0163016219633538
FOSL2#2355211.28680040304110.0100534586973120.0376536909768178
FOXA2#3170216.42030916844350.004810682352105480.0225747148711154
GATA3#2625218.15767757147070.003944546819279620.0189400269072109
HNF4A#3172215.42152690863580.005444210486686610.0246675878099376
NR3C1#290829.982015554115360.01278474365547170.046005783090439
RXRA#6256213.38307809275550.007196434429465730.0298142891577996
USF1#739136.361499277207960.00388404057290560.0189421112955259



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.