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Coexpression cluster:C3263

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Full id: C3263_testicular_uterus_large_heart_merkel_teratocarcinoma_spinal



Phase1 CAGE Peaks

Hg19::chr12:19282623..19282642,+p3@PLEKHA5
Hg19::chr12:19282643..19282710,+p1@PLEKHA5
Hg19::chr12:19282713..19282734,+p5@PLEKHA5


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
organ system subdivision6.84e-26223
central nervous system7.51e-2481
neural tube6.78e-2356
neural rod6.78e-2356
future spinal cord6.78e-2356
neural keel6.78e-2356
ectoderm-derived structure1.68e-22171
ectoderm1.68e-22171
presumptive ectoderm1.68e-22171
adult organism2.17e-21114
regional part of nervous system3.72e-2153
regional part of brain3.72e-2153
brain4.63e-2168
future brain4.63e-2168
nervous system6.72e-2189
neural plate1.90e-2082
presumptive neural plate1.90e-2082
neurectoderm7.42e-2086
anatomical cluster9.26e-20373
multi-tissue structure1.08e-19342
organ4.85e-19503
ecto-epithelium8.63e-19104
structure with developmental contribution from neural crest1.48e-18132
regional part of forebrain8.21e-1841
forebrain8.21e-1841
anterior neural tube8.21e-1841
future forebrain8.21e-1841
telencephalon4.62e-1634
brain grey matter5.07e-1634
gray matter5.07e-1634
cerebral hemisphere1.89e-1532
regional part of telencephalon2.16e-1532
pre-chordal neural plate1.14e-1461
anatomical conduit7.78e-14240
organ part7.57e-13218
cell layer2.12e-12309
epithelium3.08e-12306
multi-cellular organism5.01e-12656
cerebral cortex6.11e-1225
pallium6.11e-1225
regional part of cerebral cortex1.73e-1122
neocortex6.30e-1120
tube1.17e-10192
anatomical group1.91e-10625
anatomical system2.03e-10624
embryo1.98e-09592
digestive system2.65e-09145
digestive tract2.65e-09145
primitive gut2.65e-09145
endoderm-derived structure2.41e-08160
endoderm2.41e-08160
presumptive endoderm2.41e-08160
developing anatomical structure3.54e-07581
subdivision of digestive tract8.54e-07118
Disease
Ontology termp-valuen
carcinoma7.37e-07106


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)
MA0003.18.53684
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.17.37849
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
MA0055.13.9895
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0111.10.767139
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
MA0145.12.94723
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
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
MA0162.13.52399
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.213.8275
MA0102.21.88331
MA0258.10.519674
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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189399586152364
E2F1#186934.907389214879320.008460985347239390.0324004271140078
ELF1#199734.258097958807540.01295179875054610.0460515749058075
NANOG#79923329.24477848101273.99627955670032e-050.000734931221380921
TCF7L2#6934310.77017656313730.0008003181298398380.00612205560406818
TFAP2A#7020211.01242291536330.01054990655215560.03899839629068
TFAP2C#7022310.80922860986020.0007916746575753130.00613684476824079
YY1#752834.911170749853860.008441455341808260.0328251230338489
ZBTB7A#5134137.35190930787590.002516255860282270.0139747538310034



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.