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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,-0

Latest revision as of 11:33, 17 September 2013


Full id: C909_Whole_CD19_CD8_Neutrophils_Eosinophils_CD4_blood



Phase1 CAGE Peaks

Hg19::chr15:40600231..40600255,+p@chr15:40600231..40600255
+
Hg19::chr17:29151686..29151766,-p1@CRLF3
Hg19::chr19:18391246..18391315,+p1@AB593186
Hg19::chr19:2290149..2290192,+p2@uc002lvo.1
Hg19::chr21:44204140..44204160,+p@chr21:44204140..44204160
+
Hg19::chr2:85822676..85822691,-p@chr2:85822676..85822691
-
Hg19::chr5:162932571..162932661,+p1@MAT2B
Hg19::chr5:176784837..176784936,+p1@RGS14
Hg19::chr6:32812568..32812631,+p2@PSMB9


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

GO IDGO nameFDR corrected p-value
GO:0008831dTDP-4-dehydrorhamnose reductase activity0.00173083716001413
GO:0045226extracellular polysaccharide biosynthetic process0.00173083716001413
GO:0046379extracellular polysaccharide metabolic process0.00173083716001413
GO:0048269methionine adenosyltransferase complex0.00173083716001413
GO:0048270methionine adenosyltransferase regulator activity0.00173083716001413
GO:0006556S-adenosylmethionine biosynthetic process0.00288464368263519
GO:0046500S-adenosylmethionine metabolic process0.00370871841460287
GO:0000097sulfur amino acid biosynthetic process0.0216233659096436
GO:0000096sulfur amino acid metabolic process0.025928944303149
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.025928944303149
GO:0004298threonine endopeptidase activity0.025928944303149
GO:0033692cellular polysaccharide biosynthetic process0.025928944303149
GO:0000271polysaccharide biosynthetic process0.025928944303149
GO:0005839proteasome core complex (sensu Eukaryota)0.025928944303149
GO:0044272sulfur compound biosynthetic process0.025928944303149
GO:0000502proteasome complex (sensu Eukaryota)0.0369922818669568
GO:0044264cellular polysaccharide metabolic process0.0369922818669568
GO:0008652amino acid biosynthetic process0.0369922818669568
GO:0005976polysaccharide metabolic process0.0369922818669568
GO:0006790sulfur metabolic process0.0369922818669568
GO:0006575amino acid derivative metabolic process0.0369922818669568
GO:0043284biopolymer biosynthetic process0.0390134412752236
GO:0009968negative regulation of signal transduction0.0390134412752236
GO:0009309amine biosynthetic process0.0427614578009655
GO:0046483heterocycle metabolic process0.0448310930447899
GO:0016051carbohydrate biosynthetic process0.045748758593867
GO:0044271nitrogen compound biosynthetic process0.046045758423692
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.046045758423692
GO:0006730one-carbon compound metabolic process0.046045758423692
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0473686029795388
GO:0005057receptor signaling protein activity0.0491570475788475
GO:0006725aromatic compound metabolic process0.049226446731777



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell2.74e-63168
angioblastic mesenchymal cell2.74e-63168
hematopoietic cell1.44e-59177
hematopoietic oligopotent progenitor cell1.64e-59161
hematopoietic multipotent progenitor cell1.64e-59161
leukocyte6.08e-58136
hematopoietic lineage restricted progenitor cell1.48e-49120
nongranular leukocyte4.72e-48115
myeloid cell2.59e-33108
common myeloid progenitor2.59e-33108
myeloid leukocyte1.92e-2872
myeloid lineage restricted progenitor cell1.44e-2466
granulocyte monocyte progenitor cell1.94e-2467
nucleate cell2.83e-2455
lymphoid lineage restricted progenitor cell2.64e-2352
lymphocyte2.67e-2353
common lymphoid progenitor2.67e-2353
macrophage dendritic cell progenitor2.54e-2261
monopoietic cell5.68e-2259
monocyte5.68e-2259
monoblast5.68e-2259
promonocyte5.68e-2259
defensive cell3.34e-2048
phagocyte3.34e-2048
classical monocyte7.12e-1842
CD14-positive, CD16-negative classical monocyte7.12e-1842
T cell1.08e-1225
pro-T cell1.08e-1225
mature alpha-beta T cell4.38e-1218
alpha-beta T cell4.38e-1218
immature T cell4.38e-1218
mature T cell4.38e-1218
immature alpha-beta T cell4.38e-1218
lymphocyte of B lineage3.04e-1024
pro-B cell3.04e-1024
B cell2.06e-0914
CD8-positive, alpha-beta T cell2.00e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.60e-3298
blood island1.60e-3298
hemolymphoid system9.41e-31108
immune system1.37e-2293
bone marrow6.87e-2176
bone element1.14e-1782
adult organism5.00e-15114
skeletal element1.32e-1490
skeletal system5.15e-11100
blood8.48e-1015
haemolymphatic fluid8.48e-1015
organism substance8.48e-1015
Disease
Ontology termp-valuen
hematologic cancer8.02e-0851
immune system cancer8.02e-0851


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)
MA0003.12.34025
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.10.580022
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.11.28049
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.40898
MA0056.10
MA0057.11.37904
MA0058.10.325084
MA0059.10.865474
MA0060.11.5106
MA0061.11.98523
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.11.74484
MA0074.10.509711
MA0076.11.61616
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.10.381858
MA0093.10.73976
MA0095.10
MA0098.10
MA0100.11.30927
MA0101.10.746654
MA0103.10.257174
MA0105.12.36395
MA0106.10.554855
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.11.77226
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.11.29512
MA0139.10.808973
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.11.53859
MA0146.11.73307
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.22.62436
MA0035.20.473658
MA0039.20.483665
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.943754
MA0047.20.542971
MA0112.20.378721
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.11.77574
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
MA0018.21.36887
MA0099.20.481058
MA0079.22.36915
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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#90553.520111987201460.007045560226413870.0293956241805065
EBF1#187943.958429709586220.012557390254080.0454161194288141
ELF1#199783.784975963384486.58614701323904e-050.00106726238621516
GABPB1#255364.711789224121450.0004576307049007980.00421765735873054
MAX#414953.584753060559510.006502262485096670.0278429598885203
MYC#460974.061774789029540.0002355556796573370.00256851113256762
NFKB1#479074.268493774372980.0001696536641662860.00207306177978973
NFYA#480036.141860233276840.01048163163058090.0388188342505758
NFYB#480135.586597751178820.01358500277111940.0479520110995314
PAX5#507953.705314183987680.005616557077719420.0253934027982657
POLR2A#543081.908847268051620.0116612289598830.0425849537166061
SMARCB1#659836.084238593719140.01075671401246010.0396982386214114
SP1#666753.16576743230050.01119721686091820.0411205081661604
SPI1#668854.557957504734850.002212693387101640.0127239007078245



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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