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Coexpression cluster:C474: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:23, 17 September 2013


Full id: C474_Neutrophils_CD4_CD8_Natural_CD14_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr10:112657664..112657669,+p2@MIR4680
Hg19::chr10:27438637..27438641,-p@chr10:27438637..27438641
-
Hg19::chr10:93704937..93704948,+p@chr10:93704937..93704948
+
Hg19::chr11:11868811..11868842,+p@chr11:11868811..11868842
+
Hg19::chr12:62780642..62780650,+p@chr12:62780642..62780650
+
Hg19::chr12:76922107..76922112,-p@chr12:76922107..76922112
-
Hg19::chr15:63822540..63822544,+p@chr15:63822540..63822544
+
Hg19::chr16:11810960..11810964,-p@chr16:11810960..11810964
-
Hg19::chr1:212489954..212489959,+p@chr1:212489954..212489959
+
Hg19::chr1:235393906..235393910,-p@chr1:235393906..235393910
-
Hg19::chr21:38771224..38771228,+p@chr21:38771224..38771228
+
Hg19::chr22:40471183..40471188,+p@chr22:40471183..40471188
+
Hg19::chr2:20532166..20532170,-p@chr2:20532166..20532170
-
Hg19::chr2:42426154..42426168,+p@chr2:42426154..42426168
+
Hg19::chr3:156872939..156872954,-p14@CCNL1
Hg19::chr3:196437710..196437713,-p@chr3:196437710..196437713
-
Hg19::chr5:86704947..86704952,-p@chr5:86704947..86704952
-
Hg19::chr6:13682619..13682628,-p@chr6:13682619..13682628
-
Hg19::chr7:131063657..131063661,+p@chr7:131063657..131063661
+
Hg19::chr9:82197570..82197574,+p@chr9:82197570..82197574
+


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
leukocyte7.02e-20136
nongranular leukocyte2.16e-19115
hematopoietic lineage restricted progenitor cell7.63e-17120
hematopoietic stem cell1.83e-15168
angioblastic mesenchymal cell1.83e-15168
hematopoietic cell3.49e-15177
hematopoietic oligopotent progenitor cell1.42e-13161
hematopoietic multipotent progenitor cell1.42e-13161
myeloid leukocyte4.75e-1172
classical monocyte4.88e-1142
CD14-positive, CD16-negative classical monocyte4.88e-1142
defensive cell3.22e-1048
phagocyte3.22e-1048
myeloid lineage restricted progenitor cell1.63e-0966
nucleate cell3.90e-0955
lymphocyte4.02e-0953
common lymphoid progenitor4.02e-0953
monopoietic cell5.50e-0959
monocyte5.50e-0959
monoblast5.50e-0959
promonocyte5.50e-0959
lymphoid lineage restricted progenitor cell1.15e-0852
granulocyte monocyte progenitor cell1.50e-0867
macrophage dendritic cell progenitor2.38e-0861
CD4-positive, alpha-beta T cell2.77e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.15e-1098
blood island3.15e-1098
hemolymphoid system8.70e-09108
bone element6.41e-0782


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)
MA0003.11.12949e-07
MA0004.10.533484
MA0006.10.285338
MA0007.10.168078
MA0009.10.561062
MA0014.10.000325991
MA0017.10.342408
MA0019.10.789756
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.709504
MA0040.11.22706
MA0041.11.07308
MA0042.10.511308
MA0043.10.561349
MA0046.10.551181
MA0048.10.00760148
MA0050.10.512765
MA0051.10.251994
MA0052.10.492957
MA0055.10.000439405
MA0056.10
MA0057.10.03652
MA0058.10.380569
MA0059.10.118893
MA0060.10.0338613
MA0061.10.107862
MA0063.10
MA0066.10.255535
MA0067.10.858361
MA0068.10.370416
MA0069.10.547689
MA0070.11.32939
MA0071.10.22617
MA0072.10.533514
MA0073.14.81597e-05
MA0074.10.251422
MA0076.10.129195
MA0077.11.30604
MA0078.10.879874
MA0081.10.118989
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.350415
MA0089.10
MA0090.10.844653
MA0091.10.182521
MA0092.10.157193
MA0093.11.01605
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.0872967
MA0103.10.27232
MA0105.10.00533645
MA0106.10.28721
MA0107.10.0527035
MA0108.20.415325
MA0109.10
MA0111.10.881111
MA0113.10.300221
MA0114.10.0506063
MA0115.10.785493
MA0116.10.199654
MA0117.10.595385
MA0119.10.354175
MA0122.10.619196
MA0124.11.76576
MA0125.10.667416
MA0130.10
MA0131.10.913068
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0220308
MA0140.10.637307
MA0141.10.117869
MA0142.10.39079
MA0143.11.47497
MA0144.10.171577
MA0145.10.00274371
MA0146.10.00409937
MA0147.10.204087
MA0148.10.198049
MA0149.111.7408
MA0062.20.0239298
MA0035.20.223695
MA0039.23.52038e-06
MA0138.20.331323
MA0002.20.123692
MA0137.21.08925
MA0104.20.135419
MA0047.20.277681
MA0112.20.0023312
MA0065.20.00293392
MA0150.10.134443
MA0151.10
MA0152.10.648673
MA0153.10.65174
MA0154.10.00506877
MA0155.10.00199148
MA0156.10.0971366
MA0157.10.962803
MA0158.10
MA0159.10.0559104
MA0160.10.20889
MA0161.10
MA0162.10.00106111
MA0163.13.74282e-05
MA0164.10.310173
MA0080.20.289769
MA0018.20.288301
MA0099.20.229319
MA0079.21.17516e-10
MA0102.21.07547
MA0258.10.0413436
MA0259.10.0592752
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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