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Latest revision as of 02:28, 17 September 2013


Full id: C670_putamen_parietal_pineal_caudate_middle_occipital_cerebellum



Phase1 CAGE Peaks

Hg19::chr4:21115074..21115079,-p@chr4:21115074..21115079
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Hg19::chr4:21326759..21326765,-p@chr4:21326759..21326765
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Hg19::chr4:21385117..21385122,-p@chr4:21385117..21385122
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Hg19::chr4:21490941..21490944,-p@chr4:21490941..21490944
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Hg19::chr4:21617919..21617938,-p@chr4:21617919..21617938
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Hg19::chr4:21635843..21635847,-p@chr4:21635843..21635847
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Hg19::chr4:21698935..21698940,-p@chr4:21698935..21698940
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Hg19::chr4:21767439..21767443,-p@chr4:21767439..21767443
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Hg19::chr4:21792588..21792593,-p@chr4:21792588..21792593
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Hg19::chr4:21833284..21833287,-p@chr4:21833284..21833287
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Hg19::chr4:21923515..21923532,-p@chr4:21923515..21923532
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Hg19::chr4:21931695..21931698,-p@chr4:21931695..21931698
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Hg19::chr4:21937276..21937287,-p@chr4:21937276..21937287
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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


No GOStat results

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 system4.04e-11753
regional part of brain4.04e-11753
neural tube2.10e-11056
neural rod2.10e-11056
future spinal cord2.10e-11056
neural keel2.10e-11056
regional part of forebrain2.17e-10741
forebrain2.17e-10741
anterior neural tube2.17e-10741
future forebrain2.17e-10741
brain1.99e-10168
future brain1.99e-10168
central nervous system1.07e-8781
telencephalon2.19e-8434
brain grey matter3.56e-8434
gray matter3.56e-8434
nervous system1.81e-8189
neural plate7.24e-8082
presumptive neural plate7.24e-8082
cerebral hemisphere1.28e-7832
regional part of telencephalon3.05e-7832
pre-chordal neural plate6.00e-7861
neurectoderm1.06e-7586
regional part of cerebral cortex2.53e-7022
neocortex9.16e-6420
cerebral cortex1.62e-6125
pallium1.62e-6125
ecto-epithelium7.13e-61104
adult organism5.73e-55114
structure with developmental contribution from neural crest3.10e-48132
ectoderm-derived structure1.19e-39171
ectoderm1.19e-39171
presumptive ectoderm1.19e-39171
organ system subdivision2.40e-29223
tube3.49e-25192
basal ganglion2.30e-249
nuclear complex of neuraxis2.30e-249
aggregate regional part of brain2.30e-249
collection of basal ganglia2.30e-249
cerebral subcortex2.30e-249
diencephalon6.70e-247
future diencephalon6.70e-247
neural nucleus1.90e-239
nucleus of brain1.90e-239
gyrus1.50e-216
limbic system3.86e-185
temporal lobe3.87e-186
anatomical conduit4.38e-18240
parietal lobe5.89e-185
telencephalic nucleus9.16e-187
occipital lobe1.07e-175
regional part of diencephalon3.70e-154
organ part4.99e-15218
gland of diencephalon1.19e-144
neuroendocrine gland1.19e-144
anatomical cluster5.99e-14373
epithelium9.90e-14306
cell layer1.70e-13309
brainstem1.72e-136
segmental subdivision of hindbrain4.56e-1312
hindbrain4.56e-1312
presumptive hindbrain4.56e-1312
multi-tissue structure8.74e-13342
segmental subdivision of nervous system5.51e-1213
frontal cortex7.30e-123
pons1.56e-103
posterior neural tube2.97e-1015
chordal neural plate2.97e-1015
regional part of metencephalon1.53e-099
metencephalon1.53e-099
future metencephalon1.53e-099
corpus striatum3.53e-094
striatum3.53e-094
ventral part of telencephalon3.53e-094
future corpus striatum3.53e-094
pineal body9.58e-092
regional part of epithalamus9.58e-092
secretory circumventricular organ9.58e-092
circumventricular organ9.58e-092
epithalamus9.58e-092
organ1.37e-08503
amygdala1.79e-082
middle frontal gyrus1.79e-082
middle temporal gyrus1.99e-082
dorsal plus ventral thalamus4.07e-082
Ammon's horn4.07e-082
lobe parts of cerebral cortex4.07e-082
hippocampal formation4.07e-082
thalamic complex4.07e-082
limbic lobe4.07e-082
globus pallidus1.16e-072
pallidum1.16e-072
pituitary gland1.28e-072
embryonic structure1.32e-07564
locus ceruleus1.99e-072
brainstem nucleus1.99e-072
hindbrain nucleus1.99e-072
embryo2.85e-07592
germ layer4.19e-07560
germ layer / neural crest4.19e-07560


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)
MA0003.12.27829e-05
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.000874969
MA0017.10.199401
MA0019.11.09485
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.11.52819
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.11.52302
MA0042.11.42488
MA0043.10.725115
MA0046.10.714324
MA0048.10.0323146
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.083823
MA0056.10
MA0057.10.0301256
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
MA0061.10.0732084
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.0529803
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.16.86091e-06
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.0135703
MA0089.10
MA0090.10.682802
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.162663
MA0105.10.0255214
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.10.118142
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.0663461
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.10.0164225
MA0146.10.000600379
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.924091
MA0039.23.59348e-05
MA0138.20.474787
MA0002.20.280231
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.0147485
MA0065.20.0171659
MA0150.10.238884
MA0151.10
MA0152.10.938262
MA0153.10.820317
MA0154.10.0246626
MA0155.10.0132945
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.00205586
MA0163.10.000991488
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.938958
MA0079.23.15725e-10
MA0102.21.25596
MA0258.10.102521
MA0259.10.132107
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.