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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:53, 17 September 2013


Full id: C192_Neutrophils_CD14_Peripheral_Eosinophils_CD8_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr10:125756841..125756870,-p@chr10:125756841..125756870
-
Hg19::chr11:1882630..1882676,+p@chr11:1882630..1882676
+
Hg19::chr11:47377846..47377860,+p@chr11:47377846..47377860
+
Hg19::chr11:47378007..47378018,-p@chr11:47378007..47378018
-
Hg19::chr11:47378052..47378069,-p@chr11:47378052..47378069
-
Hg19::chr11:47378250..47378262,-p@chr11:47378250..47378262
-
Hg19::chr11:47378382..47378395,-p@chr11:47378382..47378395
-
Hg19::chr11:47378437..47378450,-p@chr11:47378437..47378450
-
Hg19::chr11:47378460..47378498,+p@chr11:47378460..47378498
+
Hg19::chr11:47378973..47378988,-p@chr11:47378973..47378988
-
Hg19::chr11:47378994..47379005,-p@chr11:47378994..47379005
-
Hg19::chr11:47379019..47379028,-p@chr11:47379019..47379028
-
Hg19::chr11:47379992..47380014,-p@chr11:47379992..47380014
-
Hg19::chr11:47402215..47402224,-p@chr11:47402215..47402224
-
Hg19::chr11:64628187..64628190,-p@chr11:64628187..64628190
-
Hg19::chr11:78112655..78112670,-p@chr11:78112655..78112670
-
Hg19::chr11:88071295..88071324,-p5@CTSC
Hg19::chr11:9268156..9268159,-p@chr11:9268156..9268159
-
Hg19::chr12:116614678..116614682,-p@chr12:116614678..116614682
-
Hg19::chr12:116645578..116645582,-p@chr12:116645578..116645582
-
Hg19::chr12:116687821..116687832,-p@chr12:116687821..116687832
-
Hg19::chr12:116712212..116712214,-p@chr12:116712212..116712214
-
Hg19::chr12:90068134..90068138,-p@chr12:90068134..90068138
-
Hg19::chr12:90098379..90098392,-p@chr12:90098379..90098392
-
Hg19::chr14:50684927..50684936,-p@chr14:50684927..50684936
-
Hg19::chr14:62177947..62177951,+p@chr14:62177947..62177951
+
Hg19::chr14:94858057..94858066,-p@chr14:94858057..94858066
-
Hg19::chr15:64985395..64985406,-p@chr15:64985395..64985406
-
Hg19::chr15:66684616..66684621,+p@chr15:66684616..66684621
+
Hg19::chr15:80355916..80355920,+p@chr15:80355916..80355920
+
Hg19::chr15:80408452..80408458,+p@chr15:80408452..80408458
+
Hg19::chr15:92411603..92411608,+p@chr15:92411603..92411608
+
Hg19::chr16:81507436..81507441,+p@chr16:81507436..81507441
+
Hg19::chr16:81569089..81569093,+p@chr16:81569089..81569093
+
Hg19::chr17:63033885..63033896,-p@chr17:63033885..63033896
-
Hg19::chr18:77682274..77682278,-p@chr18:77682274..77682278
-
Hg19::chr19:17200969..17200979,+p1@LOC100130442
Hg19::chr19:17225751..17225756,+p@chr19:17225751..17225756
+
Hg19::chr1:206868806..206868820,+p@chr1:206868806..206868820
+
Hg19::chr1:234743418..234743429,-p8@AK300375
Hg19::chr1:247581319..247581322,-p@chr1:247581319..247581322
-
Hg19::chr1:27961338..27961343,-p@chr1:27961338..27961343
-
Hg19::chr1:66805544..66805549,+p@chr1:66805544..66805549
+
Hg19::chr21:34778970..34778974,+p@chr21:34778970..34778974
+
Hg19::chr21:34800170..34800174,+p@chr21:34800170..34800174
+
Hg19::chr22:30280568..30280573,+p@chr22:30280568..30280573
+
Hg19::chr2:145240201..145240215,-p@chr2:145240201..145240215
-
Hg19::chr2:145263703..145263708,-p@chr2:145263703..145263708
-
Hg19::chr2:145267097..145267112,-p@chr2:145267097..145267112
-
Hg19::chr2:145267514..145267528,-p@chr2:145267514..145267528
-
Hg19::chr2:145272196..145272214,-p37@ZEB2
Hg19::chr2:145274038..145274052,-p31@ZEB2
Hg19::chr2:162007124..162007128,+p@chr2:162007124..162007128
+
Hg19::chr2:16829593..16829596,-p@chr2:16829593..16829596
-
Hg19::chr2:16845595..16845603,-p@chr2:16845595..16845603
-
Hg19::chr2:64328443..64328449,-p@chr2:64328443..64328449
-
Hg19::chr3:182626008..182626012,+p@chr3:182626008..182626012
+
Hg19::chr3:195096232..195096236,-p@chr3:195096232..195096236
-
Hg19::chr4:106122915..106122918,+p@chr4:106122915..106122918
+
Hg19::chr4:185727836..185727839,-p@chr4:185727836..185727839
-
Hg19::chr5:142166243..142166246,+p@chr5:142166243..142166246
+
Hg19::chr5:142172838..142172845,+p@chr5:142172838..142172845
+
Hg19::chr5:171535614..171535618,-p9@STK10
Hg19::chr5:60627654..60627666,-p@chr5:60627654..60627666
-
Hg19::chr5:74773469..74773473,-p@chr5:74773469..74773473
-
Hg19::chr5:94412147..94412155,-p@chr5:94412147..94412155
-
Hg19::chr6:108889433..108889437,+p@chr6:108889433..108889437
+
Hg19::chr6:108918111..108918115,+p@chr6:108918111..108918115
+
Hg19::chr6:14119946..14119985,+p@chr6:14119946..14119985
+
Hg19::chr6:15251164..15251175,+p@chr6:15251164..15251175
+
Hg19::chr6:15285357..15285361,+p@chr6:15285357..15285361
+
Hg19::chr6:15370582..15370586,+p@chr6:15370582..15370586
+
Hg19::chr6:15383546..15383559,+p@chr6:15383546..15383559
+
Hg19::chr6:15384618..15384622,+p@chr6:15384618..15384622
+
Hg19::chr6:15402150..15402158,+p@chr6:15402150..15402158
+
Hg19::chr6:163887231..163887256,+p@chr6:163887231..163887256
+
Hg19::chr6:18389053..18389064,+p@chr6:18389053..18389064
+
Hg19::chr6:37822761..37822764,+p@chr6:37822761..37822764
+
Hg19::chr6:37827971..37827975,+p@chr6:37827971..37827975
+
Hg19::chr7:90278480..90278521,+p@chr7:90278480..90278521
+
Hg19::chr7:99974408..99974412,+p@chr7:99974408..99974412
+
Hg19::chr8:131368773..131368783,-p@chr8:131368773..131368783
-
Hg19::chr8:56800071..56800080,+p@chr8:56800071..56800080
+
Hg19::chr8:56813118..56813123,+p@chr8:56813118..56813123
+
Hg19::chr9:33148794..33148803,-p@chr9:33148794..33148803
-
Hg19::chr9:95881097..95881117,-p@chr9:95881097..95881117
-
Hg19::chrX:19870749..19870754,-p@chrX:19870749..19870754
-
Hg19::chrX:44755886..44755889,+p@chrX:44755886..44755889
+


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:0004214dipeptidyl-peptidase I activity0.0164248079072494
GO:0046332SMAD binding0.0389894005433572
GO:0008239dipeptidyl-peptidase activity0.0389894005433572
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0389894005433572



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 monocyte9.88e-6642
CD14-positive, CD16-negative classical monocyte9.88e-6642
myeloid leukocyte4.34e-6372
defensive cell4.00e-6148
phagocyte4.00e-6148
granulocyte monocyte progenitor cell5.51e-5567
myeloid lineage restricted progenitor cell9.74e-5466
macrophage dendritic cell progenitor6.62e-5361
monopoietic cell8.52e-5359
monocyte8.52e-5359
monoblast8.52e-5359
promonocyte8.52e-5359
leukocyte1.08e-52136
nongranular leukocyte1.50e-45115
myeloid cell1.98e-45108
common myeloid progenitor1.98e-45108
hematopoietic stem cell6.79e-45168
angioblastic mesenchymal cell6.79e-45168
hematopoietic lineage restricted progenitor cell7.24e-45120
hematopoietic oligopotent progenitor cell5.39e-43161
hematopoietic multipotent progenitor cell5.39e-43161
hematopoietic cell2.28e-41177
stuff accumulating cell7.10e-2787
intermediate monocyte4.81e-159
CD14-positive, CD16-positive monocyte4.81e-159
mesenchymal cell7.25e-10354
connective tissue cell2.76e-09361
granulocyte5.63e-088
motile cell2.73e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.61e-5198
blood island1.61e-5198
bone marrow1.78e-4676
hemolymphoid system1.84e-46108
bone element1.69e-4382
immune system1.59e-4293
skeletal element4.05e-3890
skeletal system6.23e-34100
lateral plate mesoderm2.46e-17203
musculoskeletal system1.40e-14167
connective tissue1.68e-08371
adult organism9.93e-08114
neural nucleus5.87e-079
nucleus of brain5.87e-079
neural tube6.80e-0756
neural rod6.80e-0756
future spinal cord6.80e-0756
neural keel6.80e-0756
mesoderm8.59e-07315
mesoderm-derived structure8.59e-07315
presumptive mesoderm8.59e-07315
regional part of nervous system8.79e-0753
regional part of brain8.79e-0753


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
MA0004.10.0696545
MA0006.10.303933
MA0007.10.00293348
MA0009.13.94433
MA0014.13.2305e-15
MA0017.10.0945517
MA0019.12.7918
MA0024.10.0755456
MA0025.10.565898
MA0027.11.49708
MA0028.10.000302971
MA0029.10.282751
MA0030.10.57013
MA0031.10.204227
MA0038.10.160078
MA0040.11.01507
MA0041.12.17621
MA0042.10.900552
MA0043.10.384656
MA0046.10.746664
MA0048.10.0033837
MA0050.10.264265
MA0051.10.529487
MA0052.11.02648
MA0055.17.66897e-06
MA0056.10
MA0057.10.0368282
MA0058.10.0600471
MA0059.10.123936
MA0060.16.04727e-05
MA0061.10.0548933
MA0063.10
MA0066.10.321229
MA0067.10.317663
MA0068.10.00965764
MA0069.10.365832
MA0070.10.714591
MA0071.10.67839
MA0072.10.106705
MA0073.10.00453281
MA0074.10.0574926
MA0076.10.00110758
MA0077.10.688917
MA0078.10.116858
MA0081.10.124151
MA0083.10.124762
MA0084.10.46347
MA0087.10.69995
MA0088.10.00579826
MA0089.10
MA0090.10.293506
MA0091.10.160315
MA0092.10.114897
MA0093.10.0252
MA0095.10
MA0098.10
MA0100.10.0668299
MA0101.10.20687
MA0103.11.23652
MA0105.10.00310635
MA0106.10.208351
MA0107.10.0765536
MA0108.20.444249
MA0109.10
MA0111.10.192229
MA0113.10.0918597
MA0114.10.00557133
MA0115.10.263593
MA0116.10.00683179
MA0117.10.14006
MA0119.12.46734
MA0122.10.911644
MA0124.10.664495
MA0125.10.540113
MA0130.10
MA0131.10.307659
MA0132.10
MA0133.10
MA0135.13.37125
MA0136.10.167861
MA0139.10.000380916
MA0140.10.431353
MA0141.10.218575
MA0142.10.0460474
MA0143.10.0919701
MA0144.10.0543702
MA0145.10.000205942
MA0146.13.38872e-07
MA0147.10.00209674
MA0148.10.34422
MA0149.10.00722685
MA0062.21.11292e-06
MA0035.20.246214
MA0039.21.7651e-12
MA0138.20.0283091
MA0002.20.0766014
MA0137.20.145888
MA0104.20.000367435
MA0047.20.624551
MA0112.24.19236e-05
MA0065.28.54737e-05
MA0150.10.437385
MA0151.10
MA0152.11.33014
MA0153.10.516198
MA0154.10.000146656
MA0155.10.0012992
MA0156.10.000368539
MA0157.10.349672
MA0158.10
MA0159.10.0202903
MA0160.10.379637
MA0161.10
MA0162.15.76689e-05
MA0163.12.86632e-09
MA0164.10.0998171
MA0080.20.115651
MA0018.20.210085
MA0099.20.0445896
MA0079.20
MA0102.20.494276
MA0258.10.138961
MA0259.10.0976739
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

No analysis results for this cluster

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

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