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{{Coexpression_clusters
{
|full_id=C3755_CD14CD16_acute_CD19_granulocyte_CD133_CD14_Whole
 

Latest revision as of 12:32, 17 September 2013


Full id: C3755_CD14CD16_acute_CD19_granulocyte_CD133_CD14_Whole



Phase1 CAGE Peaks

Hg19::chr19:13213662..13213686,-p1@LYL1
Hg19::chr19:13213691..13213696,-p9@LYL1
Hg19::chr19:13213954..13214021,-p4@LYL1


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell2.81e-59168
angioblastic mesenchymal cell2.81e-59168
hematopoietic oligopotent progenitor cell1.99e-57161
hematopoietic multipotent progenitor cell1.99e-57161
hematopoietic cell1.42e-56177
myeloid cell4.65e-51108
common myeloid progenitor4.65e-51108
leukocyte9.75e-42136
myeloid leukocyte8.76e-4072
nongranular leukocyte1.78e-39115
hematopoietic lineage restricted progenitor cell1.40e-38120
myeloid lineage restricted progenitor cell2.91e-3666
granulocyte monocyte progenitor cell1.22e-3467
monopoietic cell5.58e-3459
monocyte5.58e-3459
monoblast5.58e-3459
promonocyte5.58e-3459
macrophage dendritic cell progenitor4.30e-3261
defensive cell5.43e-2848
phagocyte5.43e-2848
classical monocyte3.53e-2342
CD14-positive, CD16-negative classical monocyte3.53e-2342
lymphocyte of B lineage2.02e-1524
pro-B cell2.02e-1524
B cell2.16e-1114
stuff accumulating cell1.73e-1087
nucleate cell2.99e-0855
lymphocyte9.29e-0853
common lymphoid progenitor9.29e-0853
mesenchymal cell1.86e-07354
lymphoid lineage restricted progenitor cell2.66e-0752
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.46e-4098
blood island1.46e-4098
hemolymphoid system2.74e-37108
bone marrow1.67e-3076
immune system4.70e-2893
bone element2.11e-2682
adult organism1.22e-25114
skeletal element7.23e-2290
skeletal system5.11e-18100
lateral plate mesoderm3.99e-13203
blood1.61e-1015
haemolymphatic fluid1.61e-1015
organism substance1.61e-1015
neural tube5.79e-0956
neural rod5.79e-0956
future spinal cord5.79e-0956
neural keel5.79e-0956
regional part of nervous system7.40e-0853
regional part of brain7.40e-0853
Disease
Ontology termp-valuen
myeloid leukemia3.33e-1631
leukemia7.69e-1439
hematologic cancer1.15e-1351
immune system cancer1.15e-1351


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)
MA0003.13.8806
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.11.64148
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.13.5636
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.12.36034
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.14.89038
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.15.85055
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.23.41713
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.25.75024
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139168082344255
CCNT2#90536.336201576962630.003930750035764890.0189960484468673
EBF1#187938.9064668465690.00141523283560980.00914864459756452
GATA1#2623313.56030814380040.0004009615963782630.00387812818708552
JUNB#3726220.40708843988080.003131462199438740.0164485631266501
MAX#414936.452555509007120.003721913834265510.0186433073830626
MYC#460935.22228187160940.007020843755740150.0294395110212288
SIN3A#2594235.408884726815140.006318961977991520.027661416297236
SMARCA4#65972104.5106022052590.0001214518592471270.00164453659119807
SP1#666735.69838137814090.005403962701712170.0246380783430444
SPI1#668838.204323508522730.001810593189410520.0109039639089404
STAT2#6773243.50918079096040.0006968990898868230.00560864946048315
TAL1#6886219.91241111829350.003287176608740550.0170123606461969
THAP1#55145331.36914460285133.23800758564397e-050.000646728388290439
USF1#739136.361499277207960.00388404057290560.0190193789100566
USF2#7392312.99219738506960.0004558979393427810.00421507833631558
ZBTB33#10009221.10981668665410.002928597060603240.0156370014525737
ZBTB7A#5134137.35190930787590.002516255860282270.0140127570540695



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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