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Coexpression cluster:C621: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C621_Neutrophils_CD14_CD4_CD8_Natural_CD19_Eosinophils

Latest revision as of 11:27, 17 September 2013


Full id: C621_Neutrophils_CD14_CD4_CD8_Natural_CD19_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:35184811..35184815,+p@chr11:35184811..35184815
+
Hg19::chr12:89991814..89991817,-p@chr12:89991814..89991817
-
Hg19::chr14:21731417..21731450,-p@chr14:21731417..21731450
-
Hg19::chr14:21731462..21731488,-p@chr14:21731462..21731488
-
Hg19::chr14:21731634..21731651,-p@chr14:21731634..21731651
-
Hg19::chr14:21731802..21731817,-p@chr14:21731802..21731817
-
Hg19::chr14:21731966..21731989,-p@chr14:21731966..21731989
-
Hg19::chr17:60143234..60143245,-p@chr17:60143234..60143245
-
Hg19::chr19:49376985..49376996,+p17@PPP1R15A
Hg19::chr19:49377002..49377019,+p@chr19:49377002..49377019
+
Hg19::chr4:103427678..103427692,+p@chr4:103427678..103427692
+
Hg19::chr4:103436545..103436564,+p@chr4:103436545..103436564
+
Hg19::chr4:103476893..103476920,+p@chr4:103476893..103476920
+
Hg19::chr4:103506219..103506228,+p@chr4:103506219..103506228
+


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
leukocyte4.86e-41136
hematopoietic stem cell5.22e-33168
angioblastic mesenchymal cell5.22e-33168
hematopoietic lineage restricted progenitor cell1.12e-31120
hematopoietic cell1.91e-31177
nongranular leukocyte3.07e-31115
hematopoietic oligopotent progenitor cell4.19e-30161
hematopoietic multipotent progenitor cell4.19e-30161
classical monocyte1.02e-2642
CD14-positive, CD16-negative classical monocyte1.02e-2642
myeloid leukocyte2.80e-2672
defensive cell9.98e-2348
phagocyte9.98e-2348
granulocyte monocyte progenitor cell7.62e-2267
myeloid lineage restricted progenitor cell2.98e-2166
macrophage dendritic cell progenitor5.06e-2161
monopoietic cell6.53e-2059
monocyte6.53e-2059
monoblast6.53e-2059
promonocyte6.53e-2059
myeloid cell2.65e-19108
common myeloid progenitor2.65e-19108
nucleate cell2.94e-1055
lymphocyte3.86e-1053
common lymphoid progenitor3.86e-1053
lymphoid lineage restricted progenitor cell8.98e-1052
granulocyte9.09e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.30e-2098
blood island1.30e-2098
bone marrow6.32e-1976
hemolymphoid system1.01e-17108
bone element3.87e-1782
immune system1.42e-1693
skeletal element1.48e-1390
skeletal system3.12e-11100


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)
MA0003.10.000123988
MA0004.10.757232
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.00418733
MA0017.10.534321
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.953078
MA0040.10.620334
MA0041.10.792277
MA0042.10.264992
MA0043.10.69629
MA0046.11.64005
MA0048.10.0262025
MA0050.10.265714
MA0051.10.944936
MA0052.10.623986
MA0055.10.671485
MA0056.10
MA0057.10.10396
MA0058.11.09867
MA0059.10.57771
MA0060.10.0773489
MA0061.10.0626878
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.13.94404
MA0071.10.329767
MA0072.10.666958
MA0073.12.55398e-06
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0103438
MA0089.10
MA0090.10.223576
MA0091.11.39427
MA0092.10.247341
MA0093.10.915249
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.0203556
MA0106.10.399649
MA0107.10.348426
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.339925
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.12.88735
MA0136.10.966693
MA0139.10.453946
MA0140.11.572
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.10.0609666
MA0146.10.034863
MA0147.10.36013
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.21.56986
MA0039.20.00108873
MA0138.20.44894
MA0002.20.531015
MA0137.20.168782
MA0104.20.561843
MA0047.20.388882
MA0112.20.0554275
MA0065.20.333967
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.11.01572
MA0155.10.0101184
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.833266
MA0161.10
MA0162.10.00136062
MA0163.10.0498121
MA0164.10.425415
MA0080.20.915505
MA0018.20.400879
MA0099.20.886817
MA0079.20.000723295
MA0102.21.22472
MA0258.10.624652
MA0259.10.117259
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
MAFK#797535.807299958106410.01346697296069050.047573981499173
SIRT6#51548221.94834342714640.003657000215166370.0184687352742631
SMARCA4#6597222.3951290439840.003516125656802390.017852243435624



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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