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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:36, 17 September 2013


Full id: C3972_tongue_skeletal_throat_cerebellum_diaphragm_heart_medulla



Phase1 CAGE Peaks

Hg19::chr1:33336497..33336528,-p1@FNDC5
Hg19::chr1:33336544..33336561,-p2@FNDC5
Hg19::chr1:40137876..40137888,+p@chr1:40137876..40137888
+


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
adult organism4.35e-57114
neural tube9.09e-4456
neural rod9.09e-4456
future spinal cord9.09e-4456
neural keel9.09e-4456
regional part of nervous system8.52e-4153
regional part of brain8.52e-4153
brain1.89e-3968
future brain1.89e-3968
central nervous system1.28e-3881
nervous system4.52e-3689
neural plate1.06e-3482
presumptive neural plate1.06e-3482
neurectoderm3.17e-3386
regional part of forebrain7.34e-3041
forebrain7.34e-3041
anterior neural tube7.34e-3041
future forebrain7.34e-3041
ecto-epithelium4.06e-26104
structure with developmental contribution from neural crest2.94e-24132
telencephalon4.84e-2434
brain grey matter6.25e-2434
gray matter6.25e-2434
cerebral hemisphere1.17e-2232
regional part of telencephalon3.16e-2232
organ system subdivision5.92e-22223
pre-chordal neural plate1.74e-2161
ectoderm-derived structure1.02e-20171
ectoderm1.02e-20171
presumptive ectoderm1.02e-20171
regional part of cerebral cortex2.72e-1622
cerebral cortex2.93e-1625
pallium2.93e-1625
anatomical cluster1.84e-15373
posterior neural tube7.10e-1515
chordal neural plate7.10e-1515
tube1.13e-14192
neocortex1.15e-1420
anatomical conduit3.69e-14240
multi-tissue structure1.61e-12342
segmental subdivision of hindbrain4.59e-1212
hindbrain4.59e-1212
presumptive hindbrain4.59e-1212
cell layer7.18e-12309
epithelium1.76e-11306
segmental subdivision of nervous system7.74e-1113
organ3.27e-10503
neural nucleus2.56e-099
nucleus of brain2.56e-099
regional part of metencephalon4.44e-099
metencephalon4.44e-099
future metencephalon4.44e-099
multi-cellular organism1.13e-07656
telencephalic nucleus1.24e-077
basal ganglion2.33e-079
nuclear complex of neuraxis2.33e-079
aggregate regional part of brain2.33e-079
collection of basal ganglia2.33e-079
cerebral subcortex2.33e-079
brainstem2.61e-076
diencephalon2.89e-077
future diencephalon2.89e-077
gyrus3.76e-076


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.16.1256
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.90173
MA0102.21.88331
MA0258.11.29138
MA0259.10.575594
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.