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Coexpression cluster:C2360: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:04, 17 September 2013


Full id: C2360_Basophils_CD14_Mast_Natural_CD34_CD8_immature



Phase1 CAGE Peaks

Hg19::chr16:15108296..15108333,+p@chr16:15108296..15108333
+
Hg19::chr16:70060239..70060250,-p@chr16:70060239..70060250
-
Hg19::chr19:13961988..13962001,-p@chr19:13961988..13962001
-
Hg19::chr6:135819555..135819564,-p@chr6:135819555..135819564
-


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 monocyte6.25e-4742
CD14-positive, CD16-negative classical monocyte6.25e-4742
defensive cell3.45e-4448
phagocyte3.45e-4448
granulocyte monocyte progenitor cell1.59e-3967
myeloid leukocyte2.46e-3972
leukocyte9.78e-39136
macrophage dendritic cell progenitor7.60e-3761
myeloid lineage restricted progenitor cell5.87e-3566
monopoietic cell6.50e-3559
monocyte6.50e-3559
monoblast6.50e-3559
promonocyte6.50e-3559
hematopoietic lineage restricted progenitor cell6.10e-33120
nongranular leukocyte2.18e-32115
hematopoietic cell2.65e-29177
hematopoietic stem cell6.72e-29168
angioblastic mesenchymal cell6.72e-29168
stuff accumulating cell2.49e-2887
hematopoietic oligopotent progenitor cell6.09e-25161
hematopoietic multipotent progenitor cell6.09e-25161
myeloid cell9.48e-24108
common myeloid progenitor9.48e-24108
motile cell2.99e-18386
mesenchymal cell3.53e-17354
connective tissue cell9.87e-17361
multi fate stem cell1.18e-10427
intermediate monocyte2.38e-109
CD14-positive, CD16-positive monocyte2.38e-109
stem cell2.88e-10441
somatic stem cell4.68e-10433
CD4-positive, alpha-beta T cell1.77e-076
Uber Anatomy
Ontology termp-valuen
bone marrow3.03e-3776
bone element6.18e-3782
immune system5.87e-3393
hematopoietic system6.06e-3398
blood island6.06e-3398
skeletal element9.57e-3290
hemolymphoid system2.77e-31108
skeletal system1.78e-26100
connective tissue6.45e-17371
lateral plate mesoderm8.21e-11203
musculoskeletal system1.75e-09167


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.13.20374
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
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.12.49771
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.21.85039
MA0079.20.00910927
MA0102.21.75932
MA0258.11.88931
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
FOS#235336.74846648167080.005032452776317940.023463586406512
FOSL1#8061219.85678985818650.003677050009233230.0185583253232644
JUN#3725412.51282919233634.07770316866756e-050.000742323934517119
JUNB#3726215.30531632991060.006126947148475620.0270968551022505



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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