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Coexpression cluster:C1293: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:41, 17 September 2013


Full id: C1293_CD14_CD14CD16_Basophils_Mast_Eosinophils_Neutrophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:104575823..104575834,-p@chr10:104575823..104575834
-
Hg19::chr11:72431425..72431435,+p@chr11:72431425..72431435
+
Hg19::chr1:206749144..206749185,+p@chr1:206749144..206749185
+
Hg19::chr1:206749218..206749229,+p@chr1:206749218..206749229
+
Hg19::chr8:17941902..17941958,+p1@ENST00000499554
p1@ENST00000505114
p1@uc003wyp.1
Hg19::chr9:110252263..110252316,+p@chr9:110252263..110252316
+


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 monocyte1.93e-8242
CD14-positive, CD16-negative classical monocyte1.93e-8242
myeloid leukocyte6.52e-7672
defensive cell1.10e-7348
phagocyte1.10e-7348
myeloid lineage restricted progenitor cell7.61e-6266
granulocyte monocyte progenitor cell1.05e-6067
monopoietic cell9.74e-5959
monocyte9.74e-5959
monoblast9.74e-5959
promonocyte9.74e-5959
macrophage dendritic cell progenitor2.25e-5661
leukocyte2.07e-48136
myeloid cell4.16e-45108
common myeloid progenitor4.16e-45108
nongranular leukocyte1.71e-38115
stuff accumulating cell5.47e-3887
hematopoietic lineage restricted progenitor cell9.16e-38120
hematopoietic stem cell7.04e-37168
angioblastic mesenchymal cell7.04e-37168
hematopoietic cell4.79e-34177
hematopoietic oligopotent progenitor cell1.62e-33161
hematopoietic multipotent progenitor cell1.62e-33161
intermediate monocyte2.01e-199
CD14-positive, CD16-positive monocyte2.01e-199
granulocyte1.72e-128
mesenchymal cell7.35e-11354
connective tissue cell2.62e-10361
blood cell1.02e-0811
motile cell2.14e-08386
non-classical monocyte1.32e-073
CD14-low, CD16-positive monocyte1.32e-073
basophil2.81e-073
single nucleate cell6.88e-073
mononuclear cell6.88e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.31e-6198
blood island3.31e-6198
hemolymphoid system5.11e-58108
bone marrow2.86e-5676
bone element4.77e-5182
immune system4.13e-4993
skeletal element3.64e-4590
skeletal system3.87e-39100
lateral plate mesoderm1.75e-26203
musculoskeletal system1.90e-18167
mesoderm5.48e-12315
mesoderm-derived structure5.48e-12315
presumptive mesoderm5.48e-12315
connective tissue4.15e-10371
blood5.21e-0915
haemolymphatic fluid5.21e-0915
organism substance5.21e-0915


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)
MA0003.10.321379
MA0004.11.37419
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.11.935
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.11.80532
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.12.85672
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.11.50842
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.441872
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.21.50688
MA0039.21.86512
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.10.508943
MA0164.10.738243
MA0080.21.02158
MA0018.21.69036
MA0099.20.629739
MA0079.21.68161
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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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