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{{Coexpression_clusters
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Latest revision as of 11:58, 17 September 2013


Full id: C2096_cerebellum_thalamus_substantia_globus_occipital_brain_optic



Phase1 CAGE Peaks

Hg19::chr11:112834886..112834890,+p@chr11:112834886..112834890
+
Hg19::chr1:171904935..171904938,+p@chr1:171904935..171904938
+
Hg19::chr1:172001694..172001701,+p@chr1:172001694..172001701
+
Hg19::chr2:25288238..25288242,+p@chr2:25288238..25288242
+


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
neural tube3.66e-6456
neural rod3.66e-6456
future spinal cord3.66e-6456
neural keel3.66e-6456
nervous system3.79e-6089
regional part of nervous system1.00e-5953
regional part of brain1.00e-5953
central nervous system9.30e-5981
brain9.16e-5768
future brain9.16e-5768
neurectoderm1.93e-4986
neural plate3.35e-4982
presumptive neural plate3.35e-4982
regional part of forebrain7.06e-4941
forebrain7.06e-4941
anterior neural tube7.06e-4941
future forebrain7.06e-4941
adult organism5.30e-40114
brain grey matter2.08e-3934
gray matter2.08e-3934
telencephalon3.06e-3934
regional part of telencephalon1.46e-3632
cerebral hemisphere2.44e-3632
ecto-epithelium5.55e-36104
pre-chordal neural plate1.14e-3561
regional part of cerebral cortex3.09e-2922
structure with developmental contribution from neural crest1.97e-28132
ectoderm-derived structure8.29e-28171
ectoderm8.29e-28171
presumptive ectoderm8.29e-28171
cerebral cortex5.28e-2725
pallium5.28e-2725
organ system subdivision1.23e-26223
neocortex1.88e-2620
posterior neural tube8.58e-1615
chordal neural plate8.58e-1615
neural nucleus6.35e-149
nucleus of brain6.35e-149
basal ganglion7.58e-149
nuclear complex of neuraxis7.58e-149
aggregate regional part of brain7.58e-149
collection of basal ganglia7.58e-149
cerebral subcortex7.58e-149
tube9.12e-14192
anatomical cluster3.41e-13373
segmental subdivision of nervous system3.56e-1313
segmental subdivision of hindbrain9.11e-1212
hindbrain9.11e-1212
presumptive hindbrain9.11e-1212
telencephalic nucleus3.92e-117
diencephalon6.10e-117
future diencephalon6.10e-117
brainstem8.86e-106
organ part2.59e-09218
gyrus2.74e-096
multi-tissue structure4.61e-09342
anatomical conduit1.52e-08240
embryo1.74e-08592
limbic system2.34e-085
occipital lobe2.38e-085
parietal lobe2.45e-085
developing anatomical structure2.53e-08581
temporal lobe5.65e-086
regional part of metencephalon6.06e-089
metencephalon6.06e-089
future metencephalon6.06e-089
organ7.20e-08503
epithelium7.23e-08306
germ layer9.25e-08560
germ layer / neural crest9.25e-08560
embryonic tissue9.25e-08560
presumptive structure9.25e-08560
germ layer / neural crest derived structure9.25e-08560
epiblast (generic)9.25e-08560
cell layer1.30e-07309
embryonic structure1.70e-07564
regional part of diencephalon2.73e-074
multi-cellular organism6.96e-07656
anatomical system7.69e-07624
corpus striatum7.93e-074
striatum7.93e-074
ventral part of telencephalon7.93e-074
future corpus striatum7.93e-074
anatomical group8.86e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.11.73823
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.12.05538
MA0144.10.430413
MA0145.10.569905
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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.