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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:33, 17 September 2013


Full id: C899_pituitary_cerebellum_occipital_parietal_testicular_brain_temporal



Phase1 CAGE Peaks

Hg19::chr13:26042960..26043015,+p2@ATP8A2
Hg19::chr14:74185796..74185825,-p1@AK308604
Hg19::chr16:2136434..2136445,+p@chr16:2136434..2136445
+
Hg19::chr16:87369953..87369959,-p@chr16:87369953..87369959
-
Hg19::chr2:203735519..203735539,-p8@ICA1L
Hg19::chr2:203735586..203735600,-p14@ICA1L
Hg19::chr9:14662234..14662273,-p@chr9:14662234..14662273
-
Hg19::chr9:74061853..74061893,-p7@TRPM3
Hg19::chr9:74061895..74061905,-p14@TRPM3


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:0004012phospholipid-translocating ATPase activity0.0218266084661406
GO:0015247aminophospholipid transporter activity0.0218266084661406
GO:0015914phospholipid transport0.0218266084661406
GO:0015075ion transmembrane transporter activity0.0218266084661406
GO:0005548phospholipid transporter activity0.0218266084661406
GO:0022891substrate-specific transmembrane transporter activity0.0218266084661406
GO:0022857transmembrane transporter activity0.0218266084661406
GO:0022892substrate-specific transporter activity0.0222822945446405
GO:0005319lipid transporter activity0.0413879448357098
GO:0005262calcium channel activity0.0461577732564526
GO:0006869lipid transport0.0468509204505933
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0468509204505933
GO:0006816calcium ion transport0.0488370558464889
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0488370558464889
GO:0008285negative regulation of cell proliferation0.0488370558464889
GO:0006810transport0.0488370558464889
GO:0015674di-, tri-valent inorganic cation transport0.0488370558464889
GO:0051234establishment of localization0.0488370558464889
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0488370558464889
GO:0043492ATPase activity, coupled to movement of substances0.0488370558464889
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0488370558464889
GO:0051179localization0.0488370558464889
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0488370558464889
GO:0015399primary active transmembrane transporter activity0.0488370558464889



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
regional part of nervous system3.42e-8453
regional part of brain3.42e-8453
neural tube1.79e-7956
neural rod1.79e-7956
future spinal cord1.79e-7956
neural keel1.79e-7956
brain1.77e-6868
future brain1.77e-6868
central nervous system5.36e-6181
brain grey matter7.64e-6134
gray matter7.64e-6134
cerebral hemisphere3.46e-5832
regional part of forebrain9.88e-5641
forebrain9.88e-5641
anterior neural tube9.88e-5641
future forebrain9.88e-5641
telencephalon1.24e-5434
nervous system1.79e-5489
neural plate7.52e-5382
presumptive neural plate7.52e-5382
regional part of telencephalon5.93e-5232
neurectoderm3.65e-5086
regional part of cerebral cortex6.73e-4622
neocortex2.74e-4320
ecto-epithelium1.32e-40104
cerebral cortex2.84e-4025
pallium2.84e-4025
adult organism7.19e-40114
pre-chordal neural plate2.54e-3661
structure with developmental contribution from neural crest2.31e-33132
segmental subdivision of hindbrain4.50e-3012
hindbrain4.50e-3012
presumptive hindbrain4.50e-3012
segmental subdivision of nervous system1.14e-2713
ectoderm-derived structure4.52e-26171
ectoderm4.52e-26171
presumptive ectoderm4.52e-26171
posterior neural tube7.94e-2415
chordal neural plate7.94e-2415
brainstem1.35e-236
gyrus1.71e-236
regional part of metencephalon2.57e-239
metencephalon2.57e-239
future metencephalon2.57e-239
neural nucleus3.57e-229
nucleus of brain3.57e-229
organ system subdivision8.21e-22223
tube1.68e-19192
pons6.73e-183
basal ganglion1.25e-159
nuclear complex of neuraxis1.25e-159
aggregate regional part of brain1.25e-159
collection of basal ganglia1.25e-159
cerebral subcortex1.25e-159
anatomical conduit1.81e-14240
organ part1.13e-13218
temporal lobe1.36e-136
pituitary gland2.43e-132
corpus striatum3.01e-134
striatum3.01e-134
ventral part of telencephalon3.01e-134
future corpus striatum3.01e-134
telencephalic nucleus5.63e-137
locus ceruleus1.01e-122
brainstem nucleus1.01e-122
hindbrain nucleus1.01e-122
middle temporal gyrus2.29e-122
limbic system2.11e-115
occipital lobe8.93e-115
anatomical cluster1.11e-10373
parietal lobe2.00e-105
multi-tissue structure2.93e-10342
epithelium4.15e-10306
cell layer5.93e-10309
cerebellum8.33e-106
rhombic lip8.33e-106
frontal cortex8.09e-093
medulla oblongata1.96e-083
myelencephalon1.96e-083
future myelencephalon1.96e-083
caudate-putamen2.96e-083
dorsal striatum2.96e-083
insula2.52e-071
nucleus accumbens3.01e-071
ventral striatum3.01e-071
paracentral gyrus3.40e-071
olfactory region3.60e-071
primary subdivision of skull3.60e-071
cranium3.60e-071
neurocranium3.60e-071
chondrocranium3.60e-071
cartilaginous neurocranium3.60e-071
head paraxial mesoderm3.60e-071
gland of diencephalon4.44e-074
neuroendocrine gland4.44e-074
occipital pole5.78e-071
pole of cerebral hemisphere5.78e-071
putamen7.73e-071
postcentral gyrus9.73e-071


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)
MA0003.12.34025
MA0004.10.415381
MA0006.10.265592
MA0007.11.81613
MA0009.10.870971
MA0014.10.205864
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.559235
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.693769
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.9464
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.46949
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.11.31682
MA0105.10.496814
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.11.50574
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.11.31371
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.11.08897
MA0146.10.75319
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.20.674448
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.11.00468
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.11.14546
MA0160.10.453945
MA0161.10
MA0162.12.3084
MA0163.10.604232
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.741908
MA0102.21.41188
MA0258.10.532421
MA0259.10.624802
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
RAD21#588544.602237286869480.007351242900196250.0303965657317917



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.