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Coexpression cluster:C4735: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4735_Mesenchymal_Pericytes_spinal_Astrocyte_hippocampus_Osteoblast_MCF7
|id=C4735
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4735_Mesenchymal_Pericytes_spinal_Astrocyte_hippocampus_Osteoblast_MCF7



Phase1 CAGE Peaks

Hg19::chr8:145027973..145027992,-p11@PLEC
Hg19::chr8:145027995..145028012,-p9@PLEC
Hg19::chr8:145028013..145028035,-p13@PLEC


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>

Cell Type
Ontology termp-valuen
mesodermal cell2.64e-07121
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.04e-25656
anatomical system1.50e-23624
anatomical group2.68e-23625
anatomical cluster9.63e-18373
cell layer2.31e-17309
epithelium4.00e-17306
central nervous system1.80e-1681
neural plate1.00e-1582
presumptive neural plate1.00e-1582
neural tube1.51e-1556
neural rod1.51e-1556
future spinal cord1.51e-1556
neural keel1.51e-1556
tube1.84e-15192
organ1.85e-15503
anatomical conduit2.94e-15240
brain1.60e-1468
future brain1.60e-1468
embryo4.26e-14592
regional part of nervous system6.44e-1453
regional part of brain6.44e-1453
nervous system6.96e-1489
multi-tissue structure4.99e-13342
neurectoderm5.77e-1386
developing anatomical structure7.90e-13581
ecto-epithelium6.66e-12104
germ layer1.84e-11560
germ layer / neural crest1.84e-11560
embryonic tissue1.84e-11560
presumptive structure1.84e-11560
germ layer / neural crest derived structure1.84e-11560
epiblast (generic)1.84e-11560
adult organism4.30e-11114
embryonic structure4.97e-11564
structure with developmental contribution from neural crest1.30e-10132
ectoderm-derived structure1.69e-10171
ectoderm1.69e-10171
presumptive ectoderm1.69e-10171
brain grey matter7.61e-1034
gray matter7.61e-1034
organ part1.61e-09218
telencephalon1.86e-0934
organ system subdivision2.07e-09223
mesenchyme2.42e-09160
entire embryonic mesenchyme2.42e-09160
pre-chordal neural plate2.85e-0961
regional part of forebrain5.07e-0941
forebrain5.07e-0941
anterior neural tube5.07e-0941
future forebrain5.07e-0941
regional part of telencephalon6.89e-0932
posterior neural tube1.27e-0815
chordal neural plate1.27e-0815
cerebral hemisphere1.69e-0832
trunk1.02e-07199
organism subdivision2.33e-07264
cerebral cortex5.54e-0725
pallium5.54e-0725
epithelial vesicle7.52e-0778
segmental subdivision of hindbrain7.93e-0712
hindbrain7.93e-0712
presumptive hindbrain7.93e-0712
trunk mesenchyme8.48e-07122
vasculature8.56e-0778
vascular system8.56e-0778


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)
MA0003.14.57391
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.17.32221
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0039.22.15877
MA0138.21.04628
MA0002.22.08438
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.14.77883
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.62164
MA0102.21.88331
MA0258.12.22591
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285924353025109
CTCF#1066435.360256373075030.0064925092527670.0281439079338286
HMGN3#932438.178547723350590.001827766942164210.0109273657148485
MYC#460935.22228187160940.007020843755740150.0296202747326094
NRF1#4899312.21027944771090.0005492172401020010.00473694767024634
TCF7L2#6934310.77017656313730.0008003181298398380.00617634117803465
ZBTB7A#5134137.35190930787590.002516255860282270.0140992137878652



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.

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