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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: C692_Mast_Eosinophils_Neutrophils_Basophils_immature_CD4_CD19



Phase1 CAGE Peaks

Hg19::chr11:72452530..72452552,-p@chr11:72452530..72452552
-
Hg19::chr12:123373187..123373212,-p1@AK022083
Hg19::chr14:75744006..75744015,+p@chr14:75744006..75744015
+
Hg19::chr14:88471693..88471723,+p@chr14:88471693..88471723
+
Hg19::chr17:41466011..41466040,+p@chr17:41466011..41466040
+
Hg19::chr19:49377361..49377372,+p@chr19:49377361..49377372
+
Hg19::chr19:54692373..54692384,+p@chr19:54692373..54692384
+
Hg19::chr1:100818396..100818420,-p@chr1:100818396..100818420
-
Hg19::chr20:34359925..34359991,+p1@PHF20
Hg19::chr20:34361372..34361410,+p@chr20:34361372..34361410
+
Hg19::chr2:129079621..129079634,+p@chr2:129079621..129079634
+
Hg19::chr6:35311353..35311364,-p@chr6:35311353..35311364
-


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 monocyte1.14e-8142
CD14-positive, CD16-negative classical monocyte1.14e-8142
myeloid leukocyte3.24e-8172
leukocyte1.04e-74136
defensive cell6.39e-7048
phagocyte6.39e-7048
granulocyte monocyte progenitor cell2.35e-6967
hematopoietic stem cell1.14e-64168
angioblastic mesenchymal cell1.14e-64168
myeloid lineage restricted progenitor cell2.53e-6466
hematopoietic cell1.91e-60177
myeloid cell3.57e-60108
common myeloid progenitor3.57e-60108
macrophage dendritic cell progenitor4.57e-6061
hematopoietic lineage restricted progenitor cell4.66e-60120
hematopoietic oligopotent progenitor cell1.02e-59161
hematopoietic multipotent progenitor cell1.02e-59161
monopoietic cell2.60e-5659
monocyte2.60e-5659
monoblast2.60e-5659
promonocyte2.60e-5659
nongranular leukocyte9.27e-54115
stuff accumulating cell5.99e-3587
mesenchymal cell6.54e-21354
intermediate monocyte3.22e-209
CD14-positive, CD16-positive monocyte3.22e-209
connective tissue cell3.82e-20361
motile cell3.33e-18386
granulocyte1.16e-158
stem cell1.50e-14441
multi fate stem cell3.64e-14427
somatic stem cell1.03e-13433
histamine secreting cell9.94e-135
biogenic amine secreting cell9.94e-135
granulocytopoietic cell9.94e-135
mast cell9.94e-135
mast cell progenitor9.94e-135
basophil mast progenitor cell9.94e-135
blood cell5.11e-1111
basophil1.63e-083
natural killer cell3.80e-083
pro-NK cell3.80e-083
single nucleate cell6.40e-083
mononuclear cell6.40e-083
non-classical monocyte3.10e-073
CD14-low, CD16-positive monocyte3.10e-073
endocrine cell7.66e-079
Uber Anatomy
Ontology termp-valuen
bone marrow2.15e-6276
bone element7.65e-5782
hematopoietic system3.05e-5298
blood island3.05e-5298
skeletal element1.39e-5090
immune system1.63e-4893
hemolymphoid system4.46e-46108
skeletal system3.65e-44100
musculoskeletal system4.94e-21167
connective tissue4.23e-19371
lateral plate mesoderm6.67e-18203
mesoderm5.83e-08315
mesoderm-derived structure5.83e-08315
presumptive mesoderm5.83e-08315


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)
MA0003.11.91324
MA0004.10.861826
MA0006.10.552945
MA0007.11.4951
MA0009.10.756202
MA0014.10.0845458
MA0017.10.627635
MA0019.11.15437
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.641892
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.62565
MA0056.10
MA0057.10.3421
MA0058.11.25545
MA0059.11.25142
MA0060.10.103131
MA0061.12.07346
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.0136807
MA0074.11.05467
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.11.25193
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.10.291716
MA0093.11.06346
MA0095.10
MA0098.10
MA0100.11.09213
MA0101.11.69116
MA0103.10.181541
MA0105.11.2817
MA0106.10.452066
MA0107.11.3641
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.828144
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.11.97962
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.13.22091
MA0145.10.441471
MA0146.10.391218
MA0147.10.865676
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.981089
MA0039.20.117947
MA0138.20.503176
MA0002.20.316618
MA0137.20.595725
MA0104.21.13554
MA0047.20.440861
MA0112.20.681028
MA0065.20.452385
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.11.70687
MA0155.10.64751
MA0156.10.600064
MA0157.11.34413
MA0158.10
MA0159.10.867657
MA0160.10.357736
MA0161.10
MA0162.10.426994
MA0163.10.936674
MA0164.10.478818
MA0080.20.558855
MA0018.20.453345
MA0099.20.382887
MA0079.20.320683
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
CTCFL#14069046.582158119658120.00234244376012790.0132777467497421
GATA3#262549.078838785735340.0007088882425015890.0056976742464694
JUNB#372637.652658164955280.006142540980944890.0271577697700831
POLR2A#5430101.789544313798390.01056859658770230.0390522806051175
SIRT6#51548225.60640066500420.002675327429872020.0147484044047719
SPI1#668853.418468128551140.01014461279531980.0378985983592219
TAL1#688637.467154169360050.00657536370072610.0280983800957501
ZBTB7A#5134184.901272871917263.46590017012669e-050.000680020942828972



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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