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Coexpression cluster:C3200: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3200_Endothelial_Hepatic_Lymphatic_testicular_Renal_lung_Mast
|id=C3200
}}

Latest revision as of 12:21, 17 September 2013


Full id: C3200_Endothelial_Hepatic_Lymphatic_testicular_Renal_lung_Mast



Phase1 CAGE Peaks

Hg19::chr11:75062661..75062685,-p4@ARRB1
Hg19::chr11:75062686..75062723,-p1@ARRB1
Hg19::chr11:75062730..75062775,-p3@ARRB1


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
myeloid cell2.80e-27108
common myeloid progenitor2.80e-27108
myeloid leukocyte1.96e-2572
granulocyte monocyte progenitor cell3.55e-2467
myeloid lineage restricted progenitor cell2.85e-2266
monopoietic cell1.44e-2159
monocyte1.44e-2159
monoblast1.44e-2159
promonocyte1.44e-2159
macrophage dendritic cell progenitor1.86e-2161
defensive cell1.20e-2048
phagocyte1.20e-2048
endothelial cell3.24e-1836
classical monocyte2.67e-1742
CD14-positive, CD16-negative classical monocyte2.67e-1742
meso-epithelial cell2.18e-1445
endothelial cell of vascular tree1.86e-1324
stuff accumulating cell2.35e-1187
blood vessel endothelial cell7.24e-1018
embryonic blood vessel endothelial progenitor cell7.24e-1018
lining cell2.91e-0958
barrier cell2.91e-0958
hematopoietic oligopotent progenitor cell1.05e-07161
hematopoietic multipotent progenitor cell1.05e-07161
hematopoietic stem cell2.41e-07168
angioblastic mesenchymal cell2.41e-07168
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.03e-24108
adult organism2.00e-21114
immune system2.85e-2193
hematopoietic system1.18e-2098
blood island1.18e-2098
bone marrow6.61e-1976
bone element9.30e-1682
lateral plate mesoderm1.84e-12203
skeletal element6.23e-1190
blood vessel endothelium7.24e-1018
endothelium7.24e-1018
cardiovascular system endothelium7.24e-1018
neural tube9.20e-1056
neural rod9.20e-1056
future spinal cord9.20e-1056
neural keel9.20e-1056
telencephalon9.31e-1034
brain grey matter9.59e-1034
gray matter9.59e-1034
regional part of nervous system9.91e-1053
regional part of brain9.91e-1053
regional part of cerebral cortex2.98e-0922
cerebral hemisphere3.99e-0932
regional part of telencephalon4.56e-0932
skeletal system5.64e-09100
regional part of forebrain8.65e-0941
forebrain8.65e-0941
anterior neural tube8.65e-0941
future forebrain8.65e-0941
neocortex1.03e-0820
central nervous system2.01e-0881
simple squamous epithelium4.97e-0822
brain8.27e-0868
future brain8.27e-0868
mesoderm4.04e-07315
mesoderm-derived structure4.04e-07315
presumptive mesoderm4.04e-07315
squamous epithelium4.85e-0725


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)
MA0003.15.30359
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.19.33321
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.1975
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
MA0101.12.63873
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.13.02823
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
MA0139.13.97071
MA0140.10.894983
MA0141.12.84752
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.12.08673
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
MA0162.17.07944
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.15771
MA0102.21.88331
MA0258.10.519674
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
CCNT2#90536.336201576962630.003930750035764890.0189277330898266
CHD2#1106310.34402283411690.0009033701102746880.0065866427636818
CTCF#1066435.360256373075030.0064925092527670.0278468654558412
E2F1#186934.907389214879320.008460985347239390.0323849904229398
E2F6#187635.017155731697390.00791769806886330.0320671837985812
EGR1#195834.988179094810140.008056488137383440.0319248582706097
EP300#203336.77394172622320.003216880500103790.0166965402321012
HDAC2#3066313.41562023662630.0004140761399857210.00390022528715446
MYC#460935.22228187160940.007020843755740150.0293346895905643
NR3C1#2908314.9730233311730.0002978331194675480.00308065694404985
PAX5#507936.669565531177830.003370290999677260.0172391919735182
SIN3A#2594235.408884726815140.006318961977991520.0275574607491004
ZBTB7A#5134137.35190930787590.002516255860282270.0139680687675146



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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