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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:01, 17 September 2013


Full id: C2212_Mast_Eosinophils_CD34_CD14_CD19_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr12:52427064..52427075,+p@chr12:52427064..52427075
+
Hg19::chr12:52430740..52430751,-p@chr12:52430740..52430751
-
Hg19::chr12:52444766..52444777,-p@chr12:52444766..52444777
-
Hg19::chr5:179246212..179246221,+p@chr5:179246212..179246221
+


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
classical monocyte3.19e-5342
CD14-positive, CD16-negative classical monocyte3.19e-5342
defensive cell8.65e-4548
phagocyte8.65e-4548
myeloid leukocyte7.37e-4072
granulocyte monocyte progenitor cell2.23e-3767
myeloid lineage restricted progenitor cell3.67e-3666
macrophage dendritic cell progenitor1.71e-3561
monopoietic cell4.46e-3559
monocyte4.46e-3559
monoblast4.46e-3559
promonocyte4.46e-3559
leukocyte3.40e-33136
nongranular leukocyte2.86e-27115
hematopoietic lineage restricted progenitor cell6.29e-27120
hematopoietic stem cell5.42e-26168
angioblastic mesenchymal cell5.42e-26168
myeloid cell6.01e-25108
common myeloid progenitor6.01e-25108
hematopoietic cell1.24e-23177
hematopoietic oligopotent progenitor cell1.95e-21161
hematopoietic multipotent progenitor cell1.95e-21161
stuff accumulating cell4.53e-2187
intermediate monocyte1.36e-159
CD14-positive, CD16-positive monocyte1.36e-159
mesenchymal cell9.25e-14354
connective tissue cell1.48e-13361
motile cell5.18e-11386
multi fate stem cell6.41e-08427
somatic stem cell6.95e-08433
stem cell7.74e-08441
Uber Anatomy
Ontology termp-valuen
bone marrow2.25e-3676
bone element5.21e-3482
hematopoietic system8.60e-3298
blood island8.60e-3298
skeletal element6.35e-3190
immune system1.03e-3093
hemolymphoid system1.96e-28108
skeletal system1.72e-27100
connective tissue4.50e-13371
lateral plate mesoderm3.13e-12203
musculoskeletal system3.79e-11167


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)
MA0003.14.74396
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
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
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.14.13471
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.14.51896
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.18043
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
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
MA0105.17.45636
MA0106.10.869173
MA0107.12.98058
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.12.41215
MA0146.10.221129
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.22.52211
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.65877
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.97967
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
BCL11A#53335214.18472755180350.007108328585298740.0296160980221014
BHLHE40#8553222.43590677348870.002891464496853120.0156378054262774
CCNT2#90546.336201576962630.0006203100587215640.00511443611137771
CEBPB#105135.978360719368610.007153832484726970.0297191372662053
EGR1#195844.988179094810140.001615011500076050.0101303415048915
ELF1#199744.258097958807540.003041525565781240.0160625954978068
ELK4#2005312.1767612438510.0008912632577620610.006635962313924
GABPB1#255335.300762877136630.01012678824234270.0378441921223041
HMGN3#932448.178547723350590.0002234570284440470.00247771829214013
MEF2C#4208330.9835158694685.56692972943475e-050.000941241013457076
PAX5#507946.669565531177830.0005052774169483260.00443264747153853
SMARCC1#6599221.83167965981570.003051207456162050.0160909440271717
SP1#666745.69838137814090.0009482606065333980.00683144026251925
TCF12#693837.975848676639820.003090920396013070.0162732588213545
TCF7L2#693438.077632422353010.002978381685834620.0158590397107618
ZBTB7A#5134147.35190930787590.000342223540015990.00346030441434117



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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