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{{Coexpression_clusters
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0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.0343867,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;1.4709,MA0083.1;10.0819,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;2.00595,MA0108.2;2.35545,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;1.99204,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.533581,MA0156.1;2.36058,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;1.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.327251,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2952_Dendritic_xeroderma_Monocytederived_B_CD14_choriocarcinoma_splenic
|id=C2952
}}

Latest revision as of 12:16, 17 September 2013


Full id: C2952_Dendritic_xeroderma_Monocytederived_B_CD14_choriocarcinoma_splenic



Phase1 CAGE Peaks

Hg19::chrX:12885112..12885119,+p4@TLR7
Hg19::chrX:12885123..12885132,+p3@TLR7
Hg19::chrX:12885151..12885170,+p2@TLR7
Hg19::chrX:12885183..12885200,+p1@TLR7


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
nongranular leukocyte4.38e-41115
leukocyte3.48e-40136
defensive cell1.46e-3648
phagocyte1.46e-3648
hematopoietic lineage restricted progenitor cell1.99e-35120
monopoietic cell6.37e-3359
monocyte6.37e-3359
monoblast6.37e-3359
promonocyte6.37e-3359
classical monocyte1.29e-3242
CD14-positive, CD16-negative classical monocyte1.29e-3242
macrophage dendritic cell progenitor1.74e-3261
hematopoietic stem cell1.69e-30168
angioblastic mesenchymal cell1.69e-30168
granulocyte monocyte progenitor cell5.21e-2967
hematopoietic cell9.67e-29177
myeloid lineage restricted progenitor cell1.40e-2866
myeloid leukocyte1.71e-2872
hematopoietic oligopotent progenitor cell3.39e-27161
hematopoietic multipotent progenitor cell3.39e-27161
lymphocyte of B lineage2.06e-1924
pro-B cell2.06e-1924
myeloid cell1.15e-17108
common myeloid progenitor1.15e-17108
stuff accumulating cell2.38e-1387
B cell1.06e-1214
intermediate monocyte3.20e-099
CD14-positive, CD16-positive monocyte3.20e-099
lymphocyte4.14e-0953
common lymphoid progenitor4.14e-0953
lymphoid lineage restricted progenitor cell1.34e-0852
nucleate cell1.86e-0855
Uber Anatomy
Ontology termp-valuen
adult organism8.26e-45114
hematopoietic system1.68e-3698
blood island1.68e-3698
hemolymphoid system3.07e-33108
immune system1.18e-2493
bone marrow2.26e-2476
neural tube5.13e-2256
neural rod5.13e-2256
future spinal cord5.13e-2256
neural keel5.13e-2256
bone element3.10e-2182
regional part of nervous system1.24e-1953
regional part of brain1.24e-1953
skeletal element9.37e-1890
regional part of forebrain7.29e-1741
forebrain7.29e-1741
anterior neural tube7.29e-1741
future forebrain7.29e-1741
skeletal system4.96e-15100
brain grey matter9.47e-1534
gray matter9.47e-1534
telencephalon1.00e-1434
central nervous system1.86e-1481
brain6.95e-1468
future brain6.95e-1468
regional part of telencephalon2.96e-1332
cerebral hemisphere5.40e-1332
nervous system3.71e-1289
neural plate5.80e-1282
presumptive neural plate5.80e-1282
neurectoderm2.29e-1186
lateral plate mesoderm6.15e-11203
regional part of cerebral cortex3.28e-1022
blood4.38e-1015
haemolymphatic fluid4.38e-1015
organism substance4.38e-1015
neural nucleus7.69e-099
nucleus of brain7.69e-099
pre-chordal neural plate8.46e-0961
neocortex1.17e-0820
basal ganglion1.66e-089
nuclear complex of neuraxis1.66e-089
aggregate regional part of brain1.66e-089
collection of basal ganglia1.66e-089
cerebral subcortex1.66e-089
cerebral cortex2.17e-0825
pallium2.17e-0825
tissue2.30e-08773
ecto-epithelium2.89e-07104
telencephalic nucleus3.45e-077


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.11.47358
MA0059.12.50216
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.14.16323
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.110.0819
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.12.00595
MA0108.22.35545
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.21.99204
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
SPI1#668848.204323508522730.000220661881527680.0025000766158461
SRF#6722413.79717826216782.75840773062708e-050.000586254263286449
TBP#690843.706770687096390.005296377814784350.0245222504144285



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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