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Coexpression cluster:C432: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:22, 17 September 2013


Full id: C432_CD14_choriocarcinoma_Peripheral_CD34_Mast_Fibroblast_granulocyte



Phase1 CAGE Peaks

Hg19::chr12:12605663..12605676,+p@chr12:12605663..12605676
+
Hg19::chr12:12605695..12605708,+p@chr12:12605695..12605708
+
Hg19::chr12:82194544..82194548,+p@chr12:82194544..82194548
+
Hg19::chr12:82204256..82204263,+p@chr12:82204256..82204263
+
Hg19::chr16:86018820..86018823,-p@chr16:86018820..86018823
-
Hg19::chr18:3625092..3625104,+p@chr18:3625092..3625104
+
Hg19::chr1:236021384..236021389,+p@chr1:236021384..236021389
+
Hg19::chr1:94344048..94344055,-p@chr1:94344048..94344055
-
Hg19::chr3:171528432..171528445,-p5@PLD1
Hg19::chr3:197798851..197798882,-p@chr3:197798851..197798882
-
Hg19::chr3:197820053..197820077,-p@chr3:197820053..197820077
-
Hg19::chr5:171837860..171837871,+p@chr5:171837860..171837871
+
Hg19::chr5:65030399..65030409,+p@chr5:65030399..65030409
+
Hg19::chr5:77581386..77581396,+p@chr5:77581386..77581396
+
Hg19::chr5:77583788..77583798,-p@chr5:77583788..77583798
-
Hg19::chr8:133846294..133846325,+p@chr8:133846294..133846325
+
Hg19::chr8:133847581..133847588,-p@chr8:133847581..133847588
-
Hg19::chr8:133847743..133847756,+p@chr8:133847743..133847756
+
Hg19::chr8:29693127..29693132,-p@chr8:29693127..29693132
-
Hg19::chr8:39801800..39801807,+p@chr8:39801800..39801807
+
Hg19::chr8:39807228..39807234,-p@chr8:39807228..39807234
-
Hg19::chr9:15298766..15298791,+p@chr9:15298766..15298791
+
Hg19::chr9:15306169..15306172,+p@chr9:15306169..15306172
+


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 monocyte4.30e-6942
CD14-positive, CD16-negative classical monocyte4.30e-6942
defensive cell2.62e-6048
phagocyte2.62e-6048
monopoietic cell5.30e-4859
monocyte5.30e-4859
monoblast5.30e-4859
promonocyte5.30e-4859
macrophage dendritic cell progenitor2.06e-4661
myeloid lineage restricted progenitor cell7.44e-4366
granulocyte monocyte progenitor cell3.32e-4267
myeloid leukocyte3.16e-3972
stuff accumulating cell1.06e-3287
myeloid cell7.99e-26108
common myeloid progenitor7.99e-26108
nongranular leukocyte3.52e-24115
hematopoietic lineage restricted progenitor cell4.02e-23120
leukocyte2.98e-20136
hematopoietic oligopotent progenitor cell6.76e-17161
hematopoietic multipotent progenitor cell6.76e-17161
hematopoietic stem cell3.92e-16168
angioblastic mesenchymal cell3.92e-16168
hematopoietic cell3.07e-15177
mesenchymal cell8.46e-07354
Uber Anatomy
Ontology termp-valuen
bone marrow4.03e-3776
bone element2.42e-3482
skeletal element3.32e-3190
immune system3.64e-3093
hematopoietic system1.42e-2898
blood island1.42e-2898
skeletal system5.58e-28100
hemolymphoid system7.99e-26108
musculoskeletal system3.08e-16167
lateral plate mesoderm4.26e-13203
mesoderm7.36e-08315
mesoderm-derived structure7.36e-08315
presumptive mesoderm7.36e-08315


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)
MA0003.11.98041e-06
MA0004.10.888963
MA0006.10.0632578
MA0007.10.425188
MA0009.11.27126
MA0014.10.00668256
MA0017.10.583727
MA0019.10.250001
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.0703882
MA0029.11.11119
MA0030.10.425859
MA0031.10.371592
MA0038.10.21714
MA0040.10.440685
MA0041.10.483206
MA0042.10.140252
MA0043.11.27186
MA0046.11.25073
MA0048.10.0737273
MA0050.10.434675
MA0051.10.214141
MA0052.10.444013
MA0055.10.0475218
MA0056.10
MA0057.10.00365463
MA0058.10.645288
MA0059.10.642105
MA0060.10.0226691
MA0061.10.193842
MA0063.10
MA0066.10.217443
MA0067.10.802392
MA0068.10.133273
MA0069.10.497197
MA0070.10.487346
MA0071.12.37106
MA0072.11.21395
MA0073.13.2335e-08
MA0074.10.213609
MA0076.10.102323
MA0077.13.08613
MA0078.11.42963
MA0081.10.310873
MA0083.10.516887
MA0084.10.981601
MA0087.11.20936
MA0088.10.0642579
MA0089.10
MA0090.10.110205
MA0091.10.458145
MA0092.10.127244
MA0093.10.856503
MA0095.10
MA0098.10
MA0100.10.64405
MA0101.11.30976
MA0103.10.0593094
MA0105.10.0169418
MA0106.10.247115
MA0107.10.966237
MA0108.20.369058
MA0109.10
MA0111.10.117802
MA0113.10.259368
MA0114.10.331605
MA0115.10.730438
MA0116.10.0385791
MA0117.10.543727
MA0119.10.288423
MA0122.10.567011
MA0124.10.691722
MA0125.11.4911
MA0130.10
MA0131.10.302006
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.632521
MA0139.10.0139039
MA0140.10.188358
MA0141.10.637815
MA0142.12.47328
MA0143.10.7194
MA0144.10.302438
MA0145.10.0315697
MA0146.10.00423052
MA0147.10.356889
MA0148.10.4933
MA0149.10.536164
MA0062.20.0152768
MA0035.20.18788
MA0039.20.00114874
MA0138.20.78639
MA0002.20.221099
MA0137.20.543748
MA0104.20.4561
MA0047.20.238164
MA0112.20.144552
MA0065.20.0334139
MA0150.10.70627
MA0151.10
MA0152.11.07014
MA0153.10.598889
MA0154.10.0528199
MA0155.10.0240193
MA0156.10.549156
MA0157.10.864465
MA0158.10
MA0159.10.156031
MA0160.11.58042
MA0161.10
MA0162.13.33344e-05
MA0163.10.000108158
MA0164.10.268764
MA0080.20.230472
MA0018.20.248141
MA0099.24.01477
MA0079.29.8101e-13
MA0102.21.01759
MA0258.10.118144
MA0259.10.374822
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

No analysis results for this cluster

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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