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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:32, 17 September 2013


Full id: C868_Dendritic_Natural_CD8_CD4_Basophils_Eosinophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:126432739..126432751,-p7@FAM53B
Hg19::chr19:41111761..41111792,-p@chr19:41111761..41111792
-
Hg19::chr19:660790..660821,+p@chr19:660790..660821
+
Hg19::chr1:29214211..29214232,-p@chr1:29214211..29214232
-
Hg19::chr20:37434244..37434259,-p@chr20:37434244..37434259
-
Hg19::chr22:50908611..50908652,+p@chr22:50908611..50908652
+
Hg19::chr2:74757588..74757599,-p@chr2:74757588..74757599
-
Hg19::chr2:86265450..86265473,-p@chr2:86265450..86265473
-
Hg19::chr3:107809589..107809595,-p@chr3:107809589..107809595
-


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
leukocyte3.68e-41136
lymphoid lineage restricted progenitor cell3.87e-3852
lymphocyte2.74e-3753
common lymphoid progenitor2.74e-3753
hematopoietic stem cell1.53e-36168
angioblastic mesenchymal cell1.53e-36168
nucleate cell1.11e-3555
hematopoietic cell3.97e-34177
hematopoietic lineage restricted progenitor cell6.52e-30120
nongranular leukocyte7.73e-30115
hematopoietic oligopotent progenitor cell1.76e-27161
hematopoietic multipotent progenitor cell1.76e-27161
mature alpha-beta T cell1.20e-2518
alpha-beta T cell1.20e-2518
immature T cell1.20e-2518
mature T cell1.20e-2518
immature alpha-beta T cell1.20e-2518
CD4-positive, alpha-beta T cell4.91e-216
T cell1.24e-2025
pro-T cell1.24e-2025
plasmacytoid dendritic cell3.33e-123
natural killer cell3.71e-123
pro-NK cell3.71e-123
lymphocyte of B lineage7.87e-1224
pro-B cell7.87e-1224
mesenchymal cell1.47e-11354
single nucleate cell1.66e-113
mononuclear cell1.66e-113
basophil3.00e-113
naive T cell3.69e-113
connective tissue cell4.02e-11361
CD8-positive, alpha-beta T cell6.86e-1111
motile cell1.37e-09386
B cell3.42e-0814
regulatory T cell7.26e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell7.26e-082
naive regulatory T cell7.26e-082
stem cell8.78e-08441
multi fate stem cell9.90e-08427
somatic stem cell1.78e-07433
Uber Anatomy
Ontology termp-valuen
connective tissue1.58e-10371
thymus6.31e-084
hemolymphoid system gland6.31e-084
thymic region6.31e-084
pharyngeal gland6.31e-084
thymus primordium6.31e-084
hematopoietic system7.77e-0898
blood island7.77e-0898
hemolymphoid system9.83e-07108


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)
MA0003.13.57075
MA0004.10.415381
MA0006.10.265592
MA0007.11.02827
MA0009.10.870971
MA0014.10.580022
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.12.29414
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.41801
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.84474
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.11.37555
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.719601
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.12.69853
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.11.47707
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.993944
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.746654
MA0103.10.714036
MA0105.11.79761
MA0106.10.554855
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.83188
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.12.04748
MA0146.10.175555
MA0147.10.211483
MA0148.10.439278
MA0149.11.17441
MA0062.20.135498
MA0035.20.473658
MA0039.21.46687
MA0138.20.608783
MA0002.21.45266
MA0137.20.780538
MA0104.20.161609
MA0047.20.542971
MA0112.21.48222
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.842081
MA0155.10.359913
MA0156.10.785298
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.11.85802
MA0163.10.604232
MA0164.10.583138
MA0080.20.739941
MA0018.20.556211
MA0099.20.481058
MA0079.20.893499
MA0102.21.41188
MA0258.10.532421
MA0259.10.624802
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
CCNT2#90553.520111987201460.007045560226413870.0293921016371655
HMGN3#932454.543637624083660.002244618319024410.0128904482910255
TCF12#693844.726428845416190.006680355302603970.0284168144122131



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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