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{{Coexpression_clusters
{
|full_id=C4691_teratocarcinoma_carcinoid_merkel_retinoblastoma_testicular_carcinosarcoma_small
 

Latest revision as of 14:17, 17 September 2013


Full id: C4691_teratocarcinoma_carcinoid_merkel_retinoblastoma_testicular_carcinosarcoma_small



Phase1 CAGE Peaks

Hg19::chr7:64035038..64035062,+p2@uc003ttc.1
Hg19::chr7:64035065..64035085,+p1@uc003ttc.1
Hg19::chr7:64035097..64035108,+p3@uc003ttc.1


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural plate8.27e-1982
presumptive neural plate8.27e-1982
pre-chordal neural plate6.69e-1861
structure with developmental contribution from neural crest1.01e-17132
neurectoderm2.95e-1786
ecto-epithelium1.21e-14104
brain4.21e-1468
future brain4.21e-1468
ectoderm-derived structure9.40e-14171
ectoderm9.40e-14171
presumptive ectoderm9.40e-14171
central nervous system1.54e-1381
organ part4.19e-13218
regional part of nervous system6.17e-1353
regional part of brain6.17e-1353
cell layer7.83e-13309
neural tube9.48e-1356
neural rod9.48e-1356
future spinal cord9.48e-1356
neural keel9.48e-1356
telencephalon9.53e-1334
nervous system9.90e-1289
epithelium1.37e-11306
cerebral hemisphere1.43e-1132
regional part of telencephalon2.08e-1132
brain grey matter2.18e-1134
gray matter2.18e-1134
nephron epithelium6.66e-1115
renal tubule6.66e-1115
nephron tubule6.66e-1115
nephron6.66e-1115
uriniferous tubule6.66e-1115
nephrogenic mesenchyme6.66e-1115
regional part of forebrain2.64e-1041
forebrain2.64e-1041
anterior neural tube2.64e-1041
future forebrain2.64e-1041
multi-tissue structure3.40e-10342
excretory tube5.46e-1016
kidney epithelium5.46e-1016
nephron tubule epithelium7.17e-1010
cortex of kidney8.14e-1012
renal parenchyma8.14e-1012
eye8.94e-1021
visual system8.94e-1021
anatomical cluster2.89e-09373
camera-type eye3.67e-0920
simple eye3.67e-0920
immature eye3.67e-0920
ocular region3.67e-0920
eyeball of camera-type eye3.67e-0920
optic cup3.67e-0920
optic vesicle3.67e-0920
eye primordium3.67e-0920
cortex7.26e-0915
anterior segment of eyeball1.31e-0814
cerebral cortex3.64e-0825
pallium3.64e-0825
sense organ5.10e-0824
sensory system5.10e-0824
entire sense organ system5.10e-0824
face5.74e-0822
kidney7.77e-0826
kidney mesenchyme7.77e-0826
upper urinary tract7.77e-0826
kidney rudiment7.77e-0826
kidney field7.77e-0826
parenchyma2.75e-0715
vasculature of eye3.32e-076
uvea3.32e-076
vasculature of head3.32e-076
tube3.62e-07192
cavitated compound organ8.33e-0731


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.14.40988
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.12.22591
MA0259.11.40979
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
NFYB#4801316.75979325353650.0002123649923296180.00246654664523054



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.