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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0390739168378098

Latest revision as of 11:43, 17 September 2013


Full id: C1354_CD4_CD19_CD8_cord_Natural_Mast_thymus



Phase1 CAGE Peaks

Hg19::chr11:94227129..94227182,+p1@ANKRD49
Hg19::chr19:21203451..21203475,+p1@ZNF430
Hg19::chr19:21324829..21324855,+p1@ZNF431
Hg19::chr4:56814968..56815018,+p1@CEP135
Hg19::chr4:84376953..84377040,-p1@HELQ
Hg19::chr7:86781734..86781777,+p1@DMTF1


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:0006355regulation of transcription, DNA-dependent0.0283845759598042
GO:0006351transcription, DNA-dependent0.0283845759598042
GO:0032774RNA biosynthetic process0.0283845759598042
GO:0003677DNA binding0.0283845759598042
GO:0045449regulation of transcription0.0283845759598042
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0283845759598042
GO:0006350transcription0.0283845759598042
GO:0010468regulation of gene expression0.0283845759598042
GO:0031323regulation of cellular metabolic process0.0283845759598042
GO:0019222regulation of metabolic process0.0283845759598042
GO:0016070RNA metabolic process0.0283845759598042
GO:0043229intracellular organelle0.0364791675777369
GO:0043226organelle0.0364791675777369
GO:0010467gene expression0.0463822808005125
GO:0005813centrosome0.0463822808005125
GO:0050794regulation of cellular process0.0463822808005125
GO:0005815microtubule organizing center0.0463822808005125
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0463822808005125
GO:0005634nucleus0.0473610801434053
GO:0050789regulation of biological process0.0473610801434053
GO:0044424intracellular part0.0473610801434053
GO:0003676nucleic acid binding0.0485494265355204



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 cell3.35e-56168
angioblastic mesenchymal cell3.35e-56168
hematopoietic cell4.02e-52177
hematopoietic oligopotent progenitor cell8.20e-52161
hematopoietic multipotent progenitor cell8.20e-52161
leukocyte2.32e-50136
hematopoietic lineage restricted progenitor cell8.23e-42120
nongranular leukocyte3.04e-39115
myeloid cell1.63e-28108
common myeloid progenitor1.63e-28108
nucleate cell6.12e-2255
myeloid leukocyte6.62e-2272
lymphoid lineage restricted progenitor cell3.50e-2152
lymphocyte4.01e-2153
common lymphoid progenitor4.01e-2153
granulocyte monocyte progenitor cell1.64e-1967
myeloid lineage restricted progenitor cell5.20e-1966
macrophage dendritic cell progenitor3.51e-1761
monopoietic cell3.03e-1659
monocyte3.03e-1659
monoblast3.03e-1659
promonocyte3.03e-1659
classical monocyte6.94e-1642
CD14-positive, CD16-negative classical monocyte6.94e-1642
defensive cell5.30e-1548
phagocyte5.30e-1548
mature alpha-beta T cell2.06e-1118
alpha-beta T cell2.06e-1118
immature T cell2.06e-1118
mature T cell2.06e-1118
immature alpha-beta T cell2.06e-1118
T cell7.19e-1125
pro-T cell7.19e-1125
lymphocyte of B lineage6.91e-1024
pro-B cell6.91e-1024
B cell1.10e-0814
mesenchymal cell1.81e-08354
CD8-positive, alpha-beta T cell3.90e-0811
motile cell1.68e-07386
connective tissue cell3.04e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.96e-2598
blood island4.96e-2598
hemolymphoid system1.50e-21108
bone marrow2.93e-1676
immune system1.45e-1593
bone element1.08e-1482
skeletal element1.53e-1290
skeletal system1.59e-10100
adult organism2.25e-09114
blood7.75e-0815
haemolymphatic fluid7.75e-0815
organism substance7.75e-0815
connective tissue3.38e-07371
Disease
Ontology termp-valuen
hematologic cancer6.02e-0751
immune system cancer6.02e-0751


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)
MA0003.10.176622
MA0004.10.558729
MA0006.11.79433
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.12.14259
MA0025.11.17262
MA0027.12.65688
MA0028.12.77054
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.12.08473
MA0061.10.23892
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.14.17659
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.11.47313
MA0145.10.347815
MA0146.10.718193
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.24.43009
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.21.3092
MA0137.21.06611
MA0104.20.26661
MA0047.20.695777
MA0112.20.680553
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.318517
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0318308
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
CHD2#110658.620019028430714.6560374997265e-050.000814798760780724
E2F4#1874510.55671692940371.71705502564041e-050.000392573357755821
ELF1#199764.258097958807540.0001677224776288830.0020513839841999
ELK4#2005410.8237877723120.0001950599973010460.00234888401454214
GABPB1#255367.067683836182178.01905956107035e-060.000222799298084232
GTF2F1#296236.369830438378830.008068208196303160.0319143883579027
HEY1#2346264.040111043105710.0002298968555807510.00252951935313928
IRF1#365956.364303127969920.000205667514205090.00243865911853604
IRF3#3661323.49097610574480.0001836473514994550.0022235040277361
MAX#414944.301703672671410.006644923910676370.0282937544156527
MXI1#460146.64104775250620.001288516958039140.00863744689221113
NFKB1#479054.57338618682820.00102196259371130.00724348498979396
NFYA#480039.212790349915260.002822755564364270.0154486070526982
NFYB#4801411.17319550235760.0001723343348218770.00209918656338489
PAX5#507944.446377020785220.005874733519240790.0263586928734798
POLR2A#543062.147453176558070.01019570676818780.0380024774861801
RFX5#5993510.03992568932922.19894173045095e-050.000482570446284023
SIN3A#2594265.408884726815143.99207083571449e-050.000742392959421627
SP1#666743.79892091876060.01052246616798510.0389410667275501
SP2#6668313.07676524692230.001024340397937320.00725886055232567
SPI1#668845.469549005681820.00269730053614140.0148413345289538
TAF1#687263.343046285745290.0007162474284635620.00572729233453074
TAF7#687959.52755783743662.84599232912077e-050.000599742923448435
TBP#690863.706770687096390.000385416472907960.00377532461208352
TCF12#693858.862054085155354.06365504449859e-050.000743264569513815
TCF7L2#693458.975147135947793.818060286338e-050.000719773282030424
ZBTB33#10009210.55490834332710.01374250737140590.048380426325162
ZEB1#693538.444216008771930.003623843810733590.0183349783814168



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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