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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:28, 17 September 2013


Full id: C681_immature_CD14_migratory_CD34_Eosinophils_Basophils_Dendritic



Phase1 CAGE Peaks

Hg19::chr10:98460169..98460181,-p@chr10:98460169..98460181
-
Hg19::chr1:157108130..157108173,-p1@ETV3
Hg19::chr22:24899372..24899395,+p@chr22:24899372..24899395
+
Hg19::chr22:24899422..24899435,+p@chr22:24899422..24899435
+
Hg19::chr3:182887417..182887421,-p@chr3:182887417..182887421
-
Hg19::chr3:197518355..197518387,+p2@LRCH3
Hg19::chr4:142558078..142558101,+p3@IL15
Hg19::chr4:142558116..142558127,+p7@IL15
Hg19::chr4:142558137..142558151,+p4@IL15
Hg19::chr8:145086769..145086785,+p5@SPATC1
Hg19::chr8:145086786..145086804,+p6@SPATC1
Hg19::chr8:145087600..145087607,-p@chr8:145087600..145087607
-


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
classical monocyte1.26e-8542
CD14-positive, CD16-negative classical monocyte1.26e-8542
defensive cell1.28e-7748
phagocyte1.28e-7748
macrophage dendritic cell progenitor1.88e-7561
myeloid leukocyte3.14e-7572
monopoietic cell2.98e-7459
monocyte2.98e-7459
monoblast2.98e-7459
promonocyte2.98e-7459
granulocyte monocyte progenitor cell5.24e-7167
myeloid lineage restricted progenitor cell1.69e-6866
leukocyte2.29e-61136
myeloid cell6.32e-59108
common myeloid progenitor6.32e-59108
nongranular leukocyte4.01e-51115
hematopoietic stem cell8.83e-49168
angioblastic mesenchymal cell8.83e-49168
hematopoietic lineage restricted progenitor cell1.90e-48120
hematopoietic oligopotent progenitor cell1.76e-47161
hematopoietic multipotent progenitor cell1.76e-47161
hematopoietic cell1.43e-45177
stuff accumulating cell5.36e-3887
conventional dendritic cell7.22e-208
dendritic cell5.65e-1610
mesenchymal cell1.50e-15354
connective tissue cell5.70e-15361
motile cell6.27e-13386
immature conventional dendritic cell1.27e-115
common dendritic progenitor1.27e-115
intermediate monocyte7.41e-119
CD14-positive, CD16-positive monocyte7.41e-119
multi fate stem cell1.91e-10427
Langerhans cell2.00e-105
stem cell2.44e-10441
somatic stem cell4.19e-10433
basophil7.66e-093


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)
MA0003.11.34964
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.169227
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.11.10416
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.357781
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.226943
MA0056.10
MA0057.10.147728
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.12.69859
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.226673
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.0284577
MA0074.10.40963
MA0076.10.706813
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.397386
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.11.07376
MA0103.10.535462
MA0105.12.77972
MA0106.10.452066
MA0107.12.64918
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.11.97962
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0212759
MA0146.10.139505
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.21.47776
MA0035.20.376007
MA0039.21.49604
MA0138.20.503176
MA0002.21.08633
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.21.00671
MA0065.20.452385
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.12.20313
MA0155.10.0793743
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.138499
MA0163.10.688273
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.0700316
MA0102.21.28978
MA0258.11.23455
MA0259.10.149181
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
EBF1#187953.711027852737090.007149884520589760.0297252016020809
ELF1#199782.838731972538360.001804270346094040.010915610883144
ESR1#209937.692150824038620.006055325582880180.0268597217477351
MEF2C#4208310.3278386231560.002646808953776950.0146197419252967
NANOG#7992337.311194620253160.006971199585208680.0294799009385597
NFKB1#479094.116047568145382.84752237283376e-050.000599823293861205
PAX5#507973.890579893187070.0006699722807011360.00540986817876496
SPI1#668853.418468128551140.01014461279531980.0378972427560328



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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