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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:45, 17 September 2013


Full id: C1438_Basophils_CD8_Eosinophils_Natural_CD34_CD133_CD4



Phase1 CAGE Peaks

Hg19::chr18:21408652..21408682,+p@chr18:21408652..21408682
+
Hg19::chr19:45947725..45947742,+p@chr19:45947725..45947742
+
Hg19::chr4:80979943..80979995,-p@chr4:80979943..80979995
-
Hg19::chr4:80980200..80980218,+p@chr4:80980200..80980218
+
Hg19::chr7:150063162..150063212,-p@chr7:150063162..150063212
-
Hg19::chr8:37739648..37739679,+p@chr8:37739648..37739679
+


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
leukocyte1.13e-77136
hematopoietic stem cell4.23e-70168
angioblastic mesenchymal cell4.23e-70168
hematopoietic cell8.26e-67177
hematopoietic oligopotent progenitor cell5.69e-63161
hematopoietic multipotent progenitor cell5.69e-63161
hematopoietic lineage restricted progenitor cell9.02e-60120
nongranular leukocyte1.10e-58115
classical monocyte7.16e-4542
CD14-positive, CD16-negative classical monocyte7.16e-4542
myeloid leukocyte4.06e-4372
granulocyte monocyte progenitor cell7.88e-3867
defensive cell1.00e-3748
phagocyte1.00e-3748
myeloid cell1.26e-37108
common myeloid progenitor1.26e-37108
myeloid lineage restricted progenitor cell1.79e-3466
macrophage dendritic cell progenitor3.38e-3461
monopoietic cell1.31e-3159
monocyte1.31e-3159
monoblast1.31e-3159
promonocyte1.31e-3159
lymphocyte6.15e-2253
common lymphoid progenitor6.15e-2253
mesenchymal cell1.39e-21354
lymphoid lineage restricted progenitor cell5.75e-2152
nucleate cell8.66e-2155
connective tissue cell1.17e-20361
motile cell2.03e-17386
stuff accumulating cell1.12e-1587
intermediate monocyte1.28e-159
CD14-positive, CD16-positive monocyte1.28e-159
stem cell8.57e-15441
multi fate stem cell1.12e-14427
somatic stem cell4.06e-14433
CD4-positive, alpha-beta T cell6.41e-116
mature alpha-beta T cell3.81e-1018
alpha-beta T cell3.81e-1018
immature T cell3.81e-1018
mature T cell3.81e-1018
immature alpha-beta T cell3.81e-1018
lymphocyte of B lineage1.37e-0924
pro-B cell1.37e-0924
T cell5.86e-0925
pro-T cell5.86e-0925
granulocyte1.76e-088
B cell4.03e-0814
blood cell1.45e-0711
basophil5.05e-073
natural killer cell6.55e-073
pro-NK cell6.55e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.49e-3498
blood island2.49e-3498
bone marrow1.12e-3376
bone element3.48e-3082
hemolymphoid system1.20e-29108
immune system1.65e-2693
skeletal element2.90e-2690
skeletal system2.87e-22100
connective tissue2.12e-19371
lateral plate mesoderm1.96e-09203
musculoskeletal system2.30e-08167


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
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.10.7124
MA0024.12.14259
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
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.10.475586
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
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.11.54633
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
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
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.11.44958
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.413181
MA0155.10.318517
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.11.18186
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.792956
MA0102.21.58513
MA0258.10.788656
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#10538416.23853452820243.98325915717398e-050.000742340476652558
BCL11A#53335314.18472755180350.0008080831849424810.00616925436785145
CCNT2#90544.224134384641760.007109805478875810.0296139815908236
EP300#203355.644951438519330.0003688138931814860.00367088098637007
IRF4#3662310.95725634337210.001711753441810940.0106902958625422
MEF2A#420539.371615454822030.002687399947103910.0148032364491343
MEF2C#4208320.6556772463120.0002683563494060410.0028663191629799
MXI1#460146.64104775250620.001288516958039140.00863966503471041
NFKB1#479043.658708949462560.01207927289015230.0438356850958899
SMARCA4#6597252.25530110262930.0005995659215741950.00501024686216093
SPI1#668845.469549005681820.00269730053614140.0148436806140832



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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