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Coexpression cluster:C1301: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C1301_CD14CD16_CD14_CD19_myeloma_Basophils_Peripheral_Monocytederived
 

Latest revision as of 11:42, 17 September 2013


Full id: C1301_CD14CD16_CD14_CD19_myeloma_Basophils_Peripheral_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:122611224..122611295,+p2@WDR11
Hg19::chr11:60131209..60131220,+p@chr11:60131209..60131220
+
Hg19::chr11:60131239..60131261,+p@chr11:60131239..60131261
+
Hg19::chr11:63607233..63607256,-p@chr11:63607233..63607256
-
Hg19::chr14:101587625..101587634,-p@chr14:101587625..101587634
-
Hg19::chr14:23292596..23292631,-p9@SLC7A7


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

GO IDGO nameFDR corrected p-value
GO:0015171amino acid transmembrane transporter activity0.0149871322601806
GO:0006865amino acid transport0.0149871322601806
GO:0015837amine transport0.0149871322601806
GO:0046943carboxylic acid transmembrane transporter activity0.0149871322601806
GO:0046942carboxylic acid transport0.0149871322601806
GO:0005342organic acid transmembrane transporter activity0.0149871322601806
GO:0015849organic acid transport0.0149871322601806
GO:0006461protein complex assembly0.0450370893677146



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
leukocyte2.17e-72136
hematopoietic stem cell1.29e-67168
angioblastic mesenchymal cell1.29e-67168
hematopoietic oligopotent progenitor cell6.62e-63161
hematopoietic multipotent progenitor cell6.62e-63161
hematopoietic cell5.69e-62177
myeloid leukocyte1.23e-6172
nongranular leukocyte2.06e-61115
hematopoietic lineage restricted progenitor cell1.05e-60120
granulocyte monocyte progenitor cell9.97e-5667
macrophage dendritic cell progenitor1.42e-5361
myeloid lineage restricted progenitor cell6.88e-5366
monopoietic cell2.03e-5259
monocyte2.03e-5259
monoblast2.03e-5259
promonocyte2.03e-5259
myeloid cell7.01e-51108
common myeloid progenitor7.01e-51108
defensive cell4.27e-5048
phagocyte4.27e-5048
classical monocyte4.65e-4542
CD14-positive, CD16-negative classical monocyte4.65e-4542
stuff accumulating cell1.02e-1987
lymphocyte of B lineage1.40e-1924
pro-B cell1.40e-1924
mesenchymal cell4.10e-14354
B cell2.87e-1314
connective tissue cell3.66e-13361
intermediate monocyte1.07e-119
CD14-positive, CD16-positive monocyte1.07e-119
lymphocyte3.83e-1153
common lymphoid progenitor3.83e-1153
nucleate cell4.43e-1155
lymphoid lineage restricted progenitor cell1.07e-1052
motile cell6.32e-10386
granulocyte1.03e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.17e-6198
blood island9.17e-6198
hemolymphoid system1.30e-55108
bone marrow1.25e-4976
immune system1.24e-4693
bone element4.08e-4482
skeletal element3.41e-3990
skeletal system5.79e-34100
lateral plate mesoderm3.21e-17203
musculoskeletal system8.20e-13167
adult organism2.00e-12114
connective tissue2.52e-12371
blood3.89e-0915
haemolymphatic fluid3.89e-0915
organism substance3.89e-0915
tissue2.10e-07773
mesoderm6.63e-07315
mesoderm-derived structure6.63e-07315
presumptive mesoderm6.63e-07315


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.12.63632
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.11.58921
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.12.13027
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.12.35015
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.12205
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
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.11.60937
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.508943
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.0146751
MA0102.21.58513
MA0258.10.289793
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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