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{{Coexpression_clusters
{
|full_id=C992_Dendritic_melanoma_immature_CD19_Basophils_CD14_Preadipocyte
 

Latest revision as of 11:35, 17 September 2013


Full id: C992_Dendritic_melanoma_immature_CD19_Basophils_CD14_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr11:18343988..18344011,-p4@HPS5
Hg19::chr14:105528224..105528238,+p@chr14:105528224..105528238
+
Hg19::chr16:67564182..67564203,-p@chr16:67564182..67564203
-
Hg19::chr1:168195229..168195294,+p1@SFT2D2
p1@TBX19
Hg19::chr1:179051025..179051051,-p@chr1:179051025..179051051
-
Hg19::chr3:49762081..49762093,-p@chr3:49762081..49762093
-
Hg19::chr5:115420945..115420957,-p@chr5:115420945..115420957
-
Hg19::chr6:44231019..44231045,-p@chr6:44231019..44231045
-


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
leukocyte1.17e-73136
nongranular leukocyte4.34e-62115
hematopoietic lineage restricted progenitor cell2.39e-61120
hematopoietic stem cell5.50e-58168
angioblastic mesenchymal cell5.50e-58168
hematopoietic cell1.02e-54177
hematopoietic oligopotent progenitor cell1.53e-51161
hematopoietic multipotent progenitor cell1.53e-51161
myeloid leukocyte1.60e-4972
defensive cell3.29e-4848
phagocyte3.29e-4848
macrophage dendritic cell progenitor1.40e-4561
granulocyte monocyte progenitor cell2.12e-4567
classical monocyte2.06e-4442
CD14-positive, CD16-negative classical monocyte2.06e-4442
monopoietic cell4.28e-4359
monocyte4.28e-4359
monoblast4.28e-4359
promonocyte4.28e-4359
myeloid lineage restricted progenitor cell4.91e-4266
myeloid cell5.34e-33108
common myeloid progenitor5.34e-33108
stuff accumulating cell3.67e-2587
mesenchymal cell1.16e-19354
motile cell4.56e-19386
connective tissue cell1.15e-18361
lymphoid lineage restricted progenitor cell1.27e-1652
lymphocyte4.03e-1653
common lymphoid progenitor4.03e-1653
nucleate cell3.54e-1555
intermediate monocyte4.44e-139
CD14-positive, CD16-positive monocyte4.44e-139
stem cell7.67e-12441
multi fate stem cell1.60e-11427
lymphocyte of B lineage3.92e-1124
pro-B cell3.92e-1124
somatic stem cell5.84e-11433
B cell2.19e-0914
CD4-positive, alpha-beta T cell7.11e-096
Uber Anatomy
Ontology termp-valuen
bone marrow1.14e-3976
hematopoietic system3.84e-3998
blood island3.84e-3998
bone element9.57e-3782
immune system2.07e-3493
hemolymphoid system1.43e-33108
skeletal element7.91e-3290
skeletal system8.03e-27100
connective tissue2.55e-17371
lateral plate mesoderm1.38e-10203
musculoskeletal system5.38e-10167


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)
MA0003.11.66566
MA0004.12.99079
MA0006.10.300178
MA0007.11.1148
MA0009.10.918715
MA0014.11.38556
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.11.08711
MA0050.11.12793
MA0051.11.36251
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.10.632427
MA0058.14.53533
MA0059.11.69011
MA0060.10.190336
MA0061.12.19078
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.13.29705
MA0074.10.552456
MA0076.10.985027
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.14.08477
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.825856
MA0103.10.792149
MA0105.14.79011
MA0106.10.59853
MA0107.11.92372
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.11.38624
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.11.25866
MA0146.10.65158
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.21.50503
MA0035.20.515566
MA0039.21.46411
MA0138.21.57302
MA0002.20.179788
MA0137.20.86081
MA0104.21.05746
MA0047.20.586412
MA0112.20.79629
MA0065.20.226158
MA0150.11.00335
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.10.43752
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.141536
MA0164.10.627336
MA0080.20.818924
MA0018.21.46097
MA0099.20.523145
MA0079.22.23097
MA0102.21.46209
MA0258.11.13653
MA0259.10.699589
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
EBF1#187944.45323342328450.007651884996748980.0315186439430277
ELF1#199773.72583571395660.0002503412725512720.002699297146808
IRF4#3662410.95725634337210.0002614921975631970.00280217357082934
MXI1#460144.980785814379650.005094415320429170.0236985275333082
NFKB1#479085.488063424193841.21437192632393e-064.9100963845662e-05
PAX5#507965.002174148383370.0002416084515475770.00262956909870544
POU2F2#545255.691327536089080.000670954773528490.00541654522629218
REST#597844.825014358064010.005720735398269540.0257884963855263
STAT1#677237.76497031144970.005248673889186180.0243153944425442
TCF12#693867.975848676639821.63540845813217e-050.000377960663772661
USF1#739153.975937048254970.003533542098249390.0179389268519866
USF2#739246.49609869253480.001906760815928170.0112210623122061
YY1#752853.069481718658660.0112591365358360.0413333671013456
ZBTB7A#5134154.594943317422430.001819435193540470.0109018928386789
ZEB1#693536.333162006578950.009275222683824870.0350405129996739



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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