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{{Coexpression_clusters
{
|full_id=C1919_immature_CD4_Dendritic_Peripheral_Natural_migratory_CD8

Latest revision as of 11:55, 17 September 2013


Full id: C1919_immature_CD4_Dendritic_Peripheral_Natural_migratory_CD8



Phase1 CAGE Peaks

Hg19::chr3:135913298..135913322,-p7@MSL2
Hg19::chr3:16553385..16553420,-p@chr3:16553385..16553420
-
Hg19::chr3:16553696..16553720,+p@chr3:16553696..16553720
+
Hg19::chr3:16553730..16553747,+p@chr3:16553730..16553747
+
Hg19::chr3:16553761..16553777,+p@chr3:16553761..16553777
+


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
leukocyte1.27e-71136
hematopoietic cell1.35e-60177
hematopoietic stem cell8.66e-60168
angioblastic mesenchymal cell8.66e-60168
hematopoietic lineage restricted progenitor cell1.01e-56120
nongranular leukocyte6.49e-56115
hematopoietic oligopotent progenitor cell2.07e-52161
hematopoietic multipotent progenitor cell2.07e-52161
lymphoid lineage restricted progenitor cell1.93e-3952
lymphocyte1.85e-3853
common lymphoid progenitor1.85e-3853
nucleate cell1.32e-3655
classical monocyte1.30e-2142
CD14-positive, CD16-negative classical monocyte1.30e-2142
lymphocyte of B lineage8.89e-2124
pro-B cell8.89e-2124
myeloid leukocyte7.80e-2072
granulocyte monocyte progenitor cell2.46e-1967
mesenchymal cell2.30e-18354
myeloid cell5.95e-18108
common myeloid progenitor5.95e-18108
defensive cell6.58e-1848
phagocyte6.58e-1848
macrophage dendritic cell progenitor1.20e-1761
connective tissue cell1.53e-17361
myeloid lineage restricted progenitor cell1.21e-1666
monopoietic cell2.26e-1559
monocyte2.26e-1559
monoblast2.26e-1559
promonocyte2.26e-1559
T cell3.93e-1525
pro-T cell3.93e-1525
mature alpha-beta T cell6.40e-1518
alpha-beta T cell6.40e-1518
immature T cell6.40e-1518
mature T cell6.40e-1518
immature alpha-beta T cell6.40e-1518
motile cell1.13e-14386
dendritic cell2.81e-1310
B cell6.41e-1314
CD4-positive, alpha-beta T cell3.30e-126
stem cell7.25e-12441
multi fate stem cell3.16e-11427
somatic stem cell9.30e-11433
circulating cell1.15e-106
Langerhans cell2.27e-105
conventional dendritic cell5.73e-108
intermediate monocyte1.27e-089
CD14-positive, CD16-positive monocyte1.27e-089
naive T cell3.76e-073
plasmacytoid dendritic cell4.83e-073
natural killer cell5.11e-073
pro-NK cell5.11e-073
CD8-positive, alpha-beta T cell6.01e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.31e-2498
blood island2.31e-2498
hemolymphoid system6.38e-22108
immune system3.02e-1993
bone marrow4.45e-1776
connective tissue1.99e-16371
bone element4.05e-1582
skeletal element6.20e-1390
skeletal system1.58e-11100
hemopoietic organ2.52e-077
immune organ2.52e-077
Disease
Ontology termp-valuen
lymphoma6.89e-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)
MA0003.10.00991994
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.11.72991
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.12.52629
MA0145.10.143698
MA0146.10.6031
MA0147.10.386018
MA0148.12.65967
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.23.17169
MA0137.21.20193
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.83292e-05
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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#10538419.48624143384291.37275300118359e-050.000332411200302836
BCL11A#53335422.69556408288567.49488101632307e-060.000214454213277744
BCL3#602427.63768224299073.425174836939e-060.00011417868968882
CHD2#110648.275218267293490.0004028373567101730.00387902735547241
CTCF#1066444.288205098460020.005152015588243280.0239408834714367
EBF1#187958.9064668465691.78355672307702e-050.000406531821478483
ELF1#199743.406478367046030.01235066105299550.0447412656855288
EP300#203345.419153380978560.00209386927943890.0121233847253199
IRF4#3662417.53161014939532.08739444052064e-050.00046099680265074
MEF2A#4205518.74323090964414.31877656850983e-072.07093069806519e-05
MEF2C#4208433.04908359409921.68127439756556e-066.36428477011053e-05
NFKB1#479055.488063424193840.0002008162847462320.00239281825015535
PAX5#507945.335652424942260.002223389586187790.0127818894144254
POU2F2#545259.106124057742521.59639992500654e-050.000370009790873854
RAD21#588548.284027116365060.0004011622639122450.00386824722377721
RXRA#6256416.05969371130662.95432243260421e-050.000615615483916103
SIN3A#2594255.408884726815140.0002159522671657270.00248335596019834
SP1#666744.558705102512720.00407573565781680.0194910827586761
SPI1#668858.204323508522732.68916109982495e-050.000575047698821904
SRF#6722411.03774260973420.0001299255814846750.00171070320280862
TCF12#693848.507571921749140.0003614215578492260.00361314311096155
USF2#7392410.39375790805570.0001646179728687530.00202742175335374
YY1#752843.928936599883080.007193866269917620.0298533873470786



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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