Personal tools

Coexpression cluster:C2535

From FANTOM5_SSTAR

Revision as of 12:07, 17 September 2013 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Full id: C2535_hepatoblastoma_optic_locus_occipital_globus_parietal_middle



Phase1 CAGE Peaks

Hg19::chr1:16330723..16330738,+p1@C1orf64
Hg19::chr3:85327115..85327130,+p@chr3:85327115..85327130
+
Hg19::chr6:170482999..170483030,+p@chr6:170482999..170483030
+
Hg19::chr7:1130932..1130937,+p7@GPER


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:0045028purinergic nucleotide receptor activity, G-protein coupled0.0103614741551866
GO:0001608nucleotide receptor activity, G-protein coupled0.0103614741551866
GO:0016502nucleotide receptor activity0.0103614741551866
GO:0001614purinergic nucleotide receptor activity0.0103614741551866



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
adult organism6.78e-110114
neural tube3.71e-8156
neural rod3.71e-8156
future spinal cord3.71e-8156
neural keel3.71e-8156
regional part of nervous system2.47e-7553
regional part of brain2.47e-7553
regional part of forebrain3.21e-6241
forebrain3.21e-6241
anterior neural tube3.21e-6241
future forebrain3.21e-6241
central nervous system8.94e-6181
brain2.18e-6068
future brain2.18e-6068
neural plate1.76e-5882
presumptive neural plate1.76e-5882
nervous system8.81e-5689
neurectoderm4.89e-5586
brain grey matter3.59e-5334
gray matter3.59e-5334
telencephalon8.88e-5334
regional part of telencephalon4.63e-4932
cerebral hemisphere4.89e-4932
pre-chordal neural plate2.92e-4361
ecto-epithelium8.09e-43104
structure with developmental contribution from neural crest9.72e-43132
regional part of cerebral cortex4.27e-4122
neocortex5.44e-3720
cerebral cortex1.59e-3525
pallium1.59e-3525
organ system subdivision1.33e-30223
ectoderm-derived structure1.08e-28171
ectoderm1.08e-28171
presumptive ectoderm1.08e-28171
tube1.28e-22192
anatomical cluster7.30e-20373
anatomical conduit1.11e-19240
neural nucleus3.20e-199
nucleus of brain3.20e-199
basal ganglion3.71e-199
nuclear complex of neuraxis3.71e-199
aggregate regional part of brain3.71e-199
collection of basal ganglia3.71e-199
cerebral subcortex3.71e-199
posterior neural tube3.78e-1915
chordal neural plate3.78e-1915
multi-tissue structure1.33e-17342
segmental subdivision of nervous system6.94e-1613
telencephalic nucleus3.61e-157
segmental subdivision of hindbrain6.44e-1412
hindbrain6.44e-1412
presumptive hindbrain6.44e-1412
organ7.33e-14503
brainstem1.23e-136
gyrus1.83e-136
epithelium2.93e-13306
cell layer5.78e-13309
organ part1.29e-12218
limbic system1.51e-115
temporal lobe5.74e-116
parietal lobe7.11e-115
occipital lobe8.20e-115
diencephalon1.36e-107
future diencephalon1.36e-107
regional part of diencephalon3.06e-094
corpus striatum4.10e-094
striatum4.10e-094
ventral part of telencephalon4.10e-094
future corpus striatum4.10e-094
germ layer5.43e-09560
germ layer / neural crest5.43e-09560
embryonic tissue5.43e-09560
presumptive structure5.43e-09560
germ layer / neural crest derived structure5.43e-09560
epiblast (generic)5.43e-09560
developing anatomical structure6.29e-09581
embryo7.40e-09592
embryonic structure8.98e-09564
regional part of metencephalon1.48e-089
metencephalon1.48e-089
future metencephalon1.48e-089
multi-cellular organism2.37e-08656
anatomical system2.40e-08624
anatomical group2.70e-08625
frontal cortex1.11e-073
pons1.19e-073
medulla oblongata1.19e-073
myelencephalon1.19e-073
future myelencephalon1.19e-073
caudate-putamen2.72e-073
dorsal striatum2.72e-073
spinal cord3.72e-073
dorsal region element3.72e-073
dorsum3.72e-073
cardiac chamber8.59e-073


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
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
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
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
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.