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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:31, 17 September 2013


Full id: C808_Neural_spinal_cerebral_hippocampus_cerebellum_duodenum_corpus



Phase1 CAGE Peaks

Hg19::chr11:82444874..82444886,-p2@FAM181B
Hg19::chr11:82444929..82444940,-p4@FAM181B
Hg19::chr3:147657764..147657816,+p1@ENST00000467198
p1@ENST00000485006
p1@uc003ewf.1
Hg19::chr6:30848740..30848768,+p8@DDR1
Hg19::chr6:30848771..30848818,+p7@DDR1
Hg19::chr7:136936091..136936115,-p@chr7:136936091..136936115
-
Hg19::chr7:137028434..137028487,-p2@PTN
Hg19::chr7:137028498..137028519,-p6@PTN
Hg19::chr7:137028534..137028548,-p3@PTN
Hg19::chrX:70389721..70389757,+p@chrX:70389721..70389757
+


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:0007167enzyme linked receptor protein signaling pathway0.00777254054695249
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0176603039176693
GO:0007612learning0.0294277743350421
GO:0030282bone mineralization0.0294277743350421
GO:0004864protein phosphatase inhibitor activity0.0343248214812073
GO:0019212phosphatase inhibitor activity0.0343248214812073
GO:0007611learning and/or memory0.0369818444756987
GO:0008201heparin binding0.0373143987937461
GO:0019888protein phosphatase regulator activity0.0373143987937461
GO:0019208phosphatase regulator activity0.0373143987937461
GO:0007166cell surface receptor linked signal transduction0.0373143987937461
GO:0031214biomineral formation0.0373143987937461
GO:0001503ossification0.0373143987937461
GO:0046849bone remodeling0.0373143987937461
GO:0048771tissue remodeling0.0373143987937461
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0373143987937461
GO:0005539glycosaminoglycan binding0.0373143987937461
GO:0030247polysaccharide binding0.0373143987937461
GO:0001871pattern binding0.0373143987937461
GO:0019199transmembrane receptor protein kinase activity0.0373143987937461



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
neuronal stem cell7.16e-118
neural cell7.57e-1025
oligodendrocyte2.36e-087
macroglial cell2.36e-087
astrocyte2.36e-087
oligodendrocyte precursor cell2.36e-087
neuron3.95e-086
neuroblast3.95e-086
electrically signaling cell3.95e-086
neurectodermal cell8.49e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system3.07e-8181
nervous system1.31e-7889
neural tube3.25e-7056
neural rod3.25e-7056
future spinal cord3.25e-7056
neural keel3.25e-7056
regional part of nervous system7.23e-6653
regional part of brain7.23e-6653
brain1.35e-6468
future brain1.35e-6468
neural plate6.19e-6482
presumptive neural plate6.19e-6482
neurectoderm8.35e-6086
regional part of forebrain2.45e-5141
forebrain2.45e-5141
anterior neural tube2.45e-5141
future forebrain2.45e-5141
ectoderm-derived structure1.10e-49171
ectoderm1.10e-49171
presumptive ectoderm1.10e-49171
adult organism5.68e-48114
ecto-epithelium1.12e-46104
pre-chordal neural plate4.61e-4661
brain grey matter6.72e-4334
gray matter6.72e-4334
telencephalon7.57e-4334
structure with developmental contribution from neural crest1.15e-42132
regional part of telencephalon2.96e-4032
cerebral hemisphere4.70e-4032
organ system subdivision1.17e-37223
cerebral cortex1.41e-3125
pallium1.41e-3125
regional part of cerebral cortex4.77e-2822
neocortex1.36e-2520
anatomical cluster1.05e-23373
posterior neural tube3.87e-1915
chordal neural plate3.87e-1915
segmental subdivision of nervous system2.27e-1613
segmental subdivision of hindbrain3.92e-1512
hindbrain3.92e-1512
presumptive hindbrain3.92e-1512
multi-tissue structure2.81e-14342
tube5.83e-13192
neural nucleus1.33e-129
nucleus of brain1.33e-129
embryo1.69e-12592
basal ganglion1.91e-129
nuclear complex of neuraxis1.91e-129
aggregate regional part of brain1.91e-129
collection of basal ganglia1.91e-129
cerebral subcortex1.91e-129
organ part9.31e-12218
anatomical conduit3.68e-11240
regional part of metencephalon3.72e-119
metencephalon3.72e-119
future metencephalon3.72e-119
cell layer3.41e-10309
telencephalic nucleus4.64e-107
diencephalon1.05e-097
future diencephalon1.05e-097
epithelium1.07e-09306
temporal lobe1.07e-096
developing anatomical structure1.08e-09581
embryonic structure2.20e-09564
brainstem2.43e-096
germ layer3.06e-09560
germ layer / neural crest3.06e-09560
embryonic tissue3.06e-09560
presumptive structure3.06e-09560
germ layer / neural crest derived structure3.06e-09560
epiblast (generic)3.06e-09560
multi-cellular organism1.21e-08656
gyrus1.78e-086
limbic system1.50e-075
occipital lobe1.67e-075
cerebellum1.72e-076
rhombic lip1.72e-076
organ2.11e-07503
parietal lobe3.86e-075
anatomical system5.85e-07624
anatomical group6.83e-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)
MA0003.10.312279
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.462516
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
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
MA0048.10.830349
MA0050.10.965046
MA0051.10.473017
MA0052.10.753928
MA0055.13.04276
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00294698
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
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
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
MA0145.10.332712
MA0146.10.4029
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0721026
MA0138.20.569505
MA0002.20.80943
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.21.75318
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.11.12912
MA0153.10.926242
MA0154.11.12157
MA0155.11.25014
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.0728181
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.0795664
MA0102.21.36707
MA0258.11.47203
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.