Personal tools

Coexpression cluster:C743: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:30, 17 September 2013


Full id: C743_CD14_anaplastic_skeletal_submaxillary_Fibroblast_peripheral_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr11:65193524..65193532,+p2@NEAT1
Hg19::chr12:125181488..125181493,+p@chr12:125181488..125181493
+
Hg19::chr1:145244475..145244480,+p@chr1:145244475..145244480
+
Hg19::chr2:242803241..242803259,+p@chr2:242803241..242803259
+
Hg19::chr2:242803264..242803281,+p@chr2:242803264..242803281
+
Hg19::chr2:242803283..242803302,+p@chr2:242803283..242803302
+
Hg19::chr2:242803469..242803480,+p@chr2:242803469..242803480
+
Hg19::chr2:242803617..242803647,+p@chr2:242803617..242803647
+
Hg19::chr2:242803745..242803768,+p@chr2:242803745..242803768
+
Hg19::chr3:49275888..49275893,-p@chr3:49275888..49275893
-
Hg19::chr6:158217491..158217495,+p@chr6:158217491..158217495
+


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 monocyte7.45e-7642
CD14-positive, CD16-negative classical monocyte7.45e-7642
defensive cell3.92e-6548
phagocyte3.92e-6548
granulocyte monocyte progenitor cell2.02e-5167
macrophage dendritic cell progenitor2.79e-5161
monopoietic cell3.92e-5059
monocyte3.92e-5059
monoblast3.92e-5059
promonocyte3.92e-5059
myeloid lineage restricted progenitor cell2.44e-4966
myeloid leukocyte1.93e-4472
hematopoietic lineage restricted progenitor cell2.27e-36120
nongranular leukocyte9.11e-33115
myeloid cell8.76e-32108
common myeloid progenitor8.76e-32108
stuff accumulating cell1.48e-3187
leukocyte9.45e-31136
hematopoietic oligopotent progenitor cell5.00e-27161
hematopoietic multipotent progenitor cell5.00e-27161
hematopoietic cell3.01e-26177
hematopoietic stem cell2.07e-25168
angioblastic mesenchymal cell2.07e-25168
mesenchymal cell9.56e-07354
Uber Anatomy
Ontology termp-valuen
bone marrow3.46e-4476
bone element1.20e-4282
skeletal element5.77e-3890
hematopoietic system3.71e-3698
blood island3.71e-3698
immune system2.57e-3493
skeletal system3.69e-33100
hemolymphoid system7.48e-32108
musculoskeletal system7.49e-16167
lateral plate mesoderm4.12e-13203


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)
MA0003.10.000970254
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.895841
MA0043.10.790919
MA0046.10.779945
MA0048.10.41425
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.11.4122
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.126.617
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.248289
MA0089.10
MA0090.10.291627
MA0091.10.927876
MA0092.11.53836
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.11.04551
MA0141.10.726533
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.0381286
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.21.21046
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.0251803
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.245306
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.11.0031
MA0161.10
MA0162.10.00470038
MA0163.10.00253231
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.21.05945
MA0079.20.00352009
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C743&oldid=3067860"