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Coexpression cluster:C694: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:28, 17 September 2013


Full id: C694_immature_Natural_CD8_CD14_Eosinophils_Basophils_CD4



Phase1 CAGE Peaks

Hg19::chr12:122229727..122229736,-p@chr12:122229727..122229736
-
Hg19::chr15:75747267..75747285,+p@chr15:75747267..75747285
+
Hg19::chr17:66233708..66233720,+p@chr17:66233708..66233720
+
Hg19::chr1:150601870..150601890,+p@chr1:150601870..150601890
+
Hg19::chr1:151966507..151966518,+p1@ENST00000432386
p1@uc001ezm.1
Hg19::chr1:19252656..19252668,-p@chr1:19252656..19252668
-
Hg19::chr1:19803947..19803962,-p@chr1:19803947..19803962
-
Hg19::chr1:19804053..19804060,+p@chr1:19804053..19804060
+
Hg19::chr1:221884484..221884492,-p@chr1:221884484..221884492
-
Hg19::chr2:70336251..70336262,+p@chr2:70336251..70336262
+
Hg19::chr4:103421745..103421751,+p@chr4:103421745..103421751
+
Hg19::chr7:23570867..23570875,+p@chr7:23570867..23570875
+


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
leukocyte7.59e-41136
hematopoietic stem cell3.34e-33168
angioblastic mesenchymal cell3.34e-33168
hematopoietic cell4.69e-31177
hematopoietic lineage restricted progenitor cell1.39e-28120
intermediate monocyte1.08e-279
CD14-positive, CD16-positive monocyte1.08e-279
hematopoietic oligopotent progenitor cell1.79e-27161
hematopoietic multipotent progenitor cell1.79e-27161
nongranular leukocyte4.72e-26115
myeloid leukocyte7.58e-2172
granulocyte monocyte progenitor cell2.01e-1867
classical monocyte1.43e-1742
CD14-positive, CD16-negative classical monocyte1.43e-1742
myeloid cell1.12e-16108
common myeloid progenitor1.12e-16108
defensive cell6.05e-1548
phagocyte6.05e-1548
myeloid lineage restricted progenitor cell1.20e-1466
macrophage dendritic cell progenitor1.80e-1461
natural killer cell6.71e-143
pro-NK cell6.71e-143
single nucleate cell4.69e-133
mononuclear cell4.69e-133
basophil5.08e-133
monopoietic cell2.78e-1159
monocyte2.78e-1159
monoblast2.78e-1159
promonocyte2.78e-1159
mesenchymal cell6.23e-11354
lymphoid lineage restricted progenitor cell1.30e-1052
connective tissue cell1.53e-10361
lymphocyte2.33e-1053
common lymphoid progenitor2.33e-1053
nucleate cell7.05e-1055
CD1a-positive Langerhans cell9.30e-102
immature CD1a-positive Langerhans cell9.30e-102
motile cell3.62e-09386
granulocyte1.73e-088
Langerhans cell5.32e-085
mature alpha-beta T cell5.63e-0818
alpha-beta T cell5.63e-0818
immature T cell5.63e-0818
mature T cell5.63e-0818
immature alpha-beta T cell5.63e-0818
histamine secreting cell1.30e-075
biogenic amine secreting cell1.30e-075
granulocytopoietic cell1.30e-075
mast cell1.30e-075
mast cell progenitor1.30e-075
basophil mast progenitor cell1.30e-075
stem cell1.32e-07441
multi fate stem cell1.71e-07427
somatic stem cell2.91e-07433
CD4-positive, alpha-beta T cell7.27e-076
stuff accumulating cell8.61e-0787
circulating cell9.97e-076
Uber Anatomy
Ontology termp-valuen
bone marrow1.72e-1776
hematopoietic system3.26e-1798
blood island3.26e-1798
bone element7.32e-1682
hemolymphoid system4.19e-15108
skeletal element5.00e-1490
immune system2.02e-1393
skeletal system3.76e-12100
connective tissue5.22e-10371


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)
MA0003.10.0958548
MA0004.10.32225
MA0006.10.552945
MA0007.10.305951
MA0009.10.756202
MA0014.10.455267
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.06455
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.0399193
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.10.617373
MA0058.10.240796
MA0059.10.239727
MA0060.11.13897
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.226673
MA0069.10.741884
MA0070.14.20002
MA0071.10.987752
MA0072.10.726666
MA0073.10.678645
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.11.25193
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0178242
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.11.07376
MA0103.10.181541
MA0105.11.2817
MA0106.10.452066
MA0107.10.843983
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.11.29006
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.567946
MA0140.10.376643
MA0141.11.24597
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0932202
MA0146.10.391218
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.30011
MA0138.20.503176
MA0002.20.652621
MA0137.20.20663
MA0104.20.335786
MA0047.20.440861
MA0112.20.0859008
MA0065.20.452385
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.0310431
MA0155.10.962093
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.10.426994
MA0163.10.0369192
MA0164.11.20414
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.140924
MA0102.21.28978
MA0258.10.117513
MA0259.10.455773
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
EBF1#187953.711027852737090.007149884520589760.0297263849301701



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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