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{{Coexpression_clusters
{
|full_id=C1325_CD19_cord_Eosinophils_b_B_Neutrophils_acute
|

Latest revision as of 11:42, 17 September 2013


Full id: C1325_CD19_cord_Eosinophils_b_B_Neutrophils_acute



Phase1 CAGE Peaks

Hg19::chr11:102188224..102188235,+p3@BIRC3
Hg19::chr11:102188241..102188255,+p2@BIRC3
Hg19::chr17:38020392..38020477,-p1@IKZF3
Hg19::chr2:231090344..231090361,-p3@SP110
Hg19::chr2:231090433..231090469,+p1@SP140
Hg19::chr2:231090471..231090504,+p2@SP140


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:0008270zinc ion binding0.0136564976516669
GO:0046914transition metal ion binding0.0136564976516669
GO:0005062hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity0.0136564976516669
GO:0005634nucleus0.021856297443892
GO:0043169cation binding0.021856297443892
GO:0046872metal ion binding0.021856297443892
GO:0043167ion binding0.021856297443892
GO:0003677DNA binding0.0396340780388288
GO:0043231intracellular membrane-bound organelle0.0396340780388288
GO:0043227membrane-bound organelle0.0396340780388288
GO:0007498mesoderm development0.0408971864373122



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
leukocyte4.82e-76136
nongranular leukocyte1.79e-62115
hematopoietic lineage restricted progenitor cell2.51e-60120
hematopoietic stem cell1.53e-53168
angioblastic mesenchymal cell1.53e-53168
hematopoietic cell2.73e-52177
hematopoietic oligopotent progenitor cell1.32e-50161
hematopoietic multipotent progenitor cell1.32e-50161
lymphocyte3.03e-3653
common lymphoid progenitor3.03e-3653
lymphoid lineage restricted progenitor cell2.27e-3552
nucleate cell5.57e-3455
myeloid leukocyte1.21e-3072
granulocyte monocyte progenitor cell4.99e-2567
defensive cell7.20e-2548
phagocyte7.20e-2548
macrophage dendritic cell progenitor5.61e-2461
myeloid lineage restricted progenitor cell1.81e-2366
classical monocyte2.81e-2342
CD14-positive, CD16-negative classical monocyte2.81e-2342
monopoietic cell3.85e-2359
monocyte3.85e-2359
monoblast3.85e-2359
promonocyte3.85e-2359
lymphocyte of B lineage1.12e-1824
pro-B cell1.12e-1824
myeloid cell8.10e-18108
common myeloid progenitor8.10e-18108
T cell2.42e-1525
pro-T cell2.42e-1525
mature alpha-beta T cell2.20e-1418
alpha-beta T cell2.20e-1418
immature T cell2.20e-1418
mature T cell2.20e-1418
immature alpha-beta T cell2.20e-1418
B cell2.57e-1114
CD8-positive, alpha-beta T cell3.18e-0911
granulocyte2.33e-078
stuff accumulating cell4.62e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.31e-3498
blood island5.31e-3498
hemolymphoid system3.59e-30108
immune system4.72e-2193
bone marrow2.31e-2076
bone element5.60e-1882
adult organism1.86e-14114
skeletal element1.98e-1490
skeletal system1.88e-11100
blood1.97e-1115
haemolymphatic fluid1.97e-1115
organism substance1.97e-1115
lateral plate mesoderm8.66e-07203
Disease
Ontology termp-valuen
lymphoma3.96e-0710


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
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
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.13.56768
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.216116
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.12.02016
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.11.62836
MA0101.11.81721
MA0103.10.993014
MA0105.12.61648
MA0106.10.70837
MA0107.13.24579
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.12.43882
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
MA0144.10.299851
MA0145.10.347815
MA0146.10.0213085
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.680553
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.02158
MA0018.21.69036
MA0099.20.629739
MA0079.20.00575781
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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
BATF#10538312.17890089615180.00125981487125340.00846079386141299
BCL11A#53335314.18472755180350.0008080831849424810.00616835256192134
BCLAF1#9774310.82632380506090.001772351046991060.0108877460735663
EBF1#187957.422055705474179.7002838805275e-050.00137966491651697
ELF1#199764.258097958807540.0001677224776288830.00205090362265343
FOXA1#316935.540709874692730.01192178777860280.0433741933327353
GATA1#262336.780154071900220.006765763983348560.0287450014098503
IRF4#3662518.26209390562011.14070523243612e-064.65913624444255e-05
MEF2A#420539.371615454822030.002687399947103910.0147977731362675
NFKB1#479065.488063424193843.65870229532191e-050.000706827985610664
NRF1#489936.105139723855450.009090162079396740.0343998636644002
PAX5#507966.669565531177831.13557256338955e-050.000289758277419597
POLR2A#543062.147453176558070.01019570676818780.0379902750423763
POU2F2#545269.106124057742521.75272139021506e-066.59648537919533e-05
RFX5#5993510.03992568932922.19894173045095e-050.000482469065938165
SMC3#912637.522466422466420.005039540716828550.0234798622825151
SRF#672236.89858913108390.00644245168930370.0279989684981561
TAF1#687263.343046285745290.0007162474284635620.00572510065676611
TBP#690853.088975572580320.006645448275786930.0282809980226931
TCF12#693835.317232451093210.013367345733860.0472396109057829
TCF7L2#693435.385088281568670.01290488779931040.0463997513296442
USF2#739248.661464923379730.0004635355081435620.00426755861556818
YY1#752864.911170749853867.12445972864136e-050.00112346587588642



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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