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Coexpression cluster:C213: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:57, 17 September 2013


Full id: C213_CD14_Natural_CD8_CD4_Basophils_Eosinophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:102130575..102130607,+p@chr10:102130575..102130607
+
Hg19::chr10:105881496..105881525,-p@chr10:105881496..105881525
-
Hg19::chr10:127730695..127730726,+p@chr10:127730695..127730726
+
Hg19::chr10:17248566..17248644,+p@chr10:17248566..17248644
+
Hg19::chr10:17270419..17270434,-p@chr10:17270419..17270434
-
Hg19::chr10:33269613..33269628,+p@chr10:33269613..33269628
+
Hg19::chr10:33269657..33269672,+p@chr10:33269657..33269672
+
Hg19::chr10:3825708..3825723,+p@chr10:3825708..3825723
+
Hg19::chr10:3826863..3826874,-p@chr10:3826863..3826874
-
Hg19::chr10:3847651..3847673,+p@chr10:3847651..3847673
+
Hg19::chr10:3847675..3847688,+p@chr10:3847675..3847688
+
Hg19::chr10:90753989..90754005,-p@chr10:90753989..90754005
-
Hg19::chr11:102187946..102187979,-p@chr11:102187946..102187979
-
Hg19::chr12:122224417..122224427,+p@chr12:122224417..122224427
+
Hg19::chr12:122228022..122228041,+p@chr12:122228022..122228041
+
Hg19::chr12:65563377..65563392,+p2@LEMD3
Hg19::chr12:76478857..76478871,+p@chr12:76478857..76478871
+
Hg19::chr12:96793473..96793491,+p@chr12:96793473..96793491
+
Hg19::chr13:114896468..114896497,-p@chr13:114896468..114896497
-
Hg19::chr13:47128179..47128209,-p@chr13:47128179..47128209
-
Hg19::chr13:99934915..99934930,-p@chr13:99934915..99934930
-
Hg19::chr14:70233907..70233918,+p2@SRSF5
Hg19::chr14:77422765..77422782,-p@chr14:77422765..77422782
-
Hg19::chr14:93049440..93049476,-p@chr14:93049440..93049476
-
Hg19::chr15:42229070..42229082,+p@chr15:42229070..42229082
+
Hg19::chr16:15737263..15737283,+p2@NDE1
Hg19::chr17:2498730..2498733,+p@chr17:2498730..2498733
+
Hg19::chr17:33570639..33570656,-p@chr17:33570639..33570656
-
Hg19::chr17:7744740..7744755,-p@chr17:7744740..7744755
-
Hg19::chr17:8867066..8867104,-p@chr17:8867066..8867104
-
Hg19::chr18:11851090..11851103,+p5@CHMP1B
Hg19::chr18:57572110..57572120,-p@chr18:57572110..57572120
-
Hg19::chr19:14229527..14229543,-p@chr19:14229527..14229543
-
Hg19::chr19:44099470..44099492,+p@chr19:44099470..44099492
+
Hg19::chr1:15735925..15735938,-p2@ENST00000427824
Hg19::chr1:171453206..171453207,-p@chr1:171453206..171453207
-
Hg19::chr1:2187769..2187789,+p@chr1:2187769..2187789
+
Hg19::chr1:235490525..235490573,+p5@GGPS1
Hg19::chr1:54872206..54872236,+p@chr1:54872206..54872236
+
Hg19::chr1:59250046..59250065,+p@chr1:59250046..59250065
+
Hg19::chr1:59281989..59282008,-p@chr1:59281989..59282008
-
Hg19::chr20:35201225..35201242,-p@chr20:35201225..35201242
-
Hg19::chr20:56881907..56881918,-p@chr20:56881907..56881918
-
Hg19::chr21:43653871..43653885,+p@chr21:43653871..43653885
+
Hg19::chr21:43654826..43654849,-p@chr21:43654826..43654849
-
Hg19::chr2:161263682..161263696,+p@chr2:161263682..161263696
+
Hg19::chr2:178077094..178077105,-p@chr2:178077094..178077105
-
Hg19::chr2:97203110..97203159,+p4@ARID5A
Hg19::chr3:119013380..119013388,-p@chr3:119013380..119013388
-
Hg19::chr3:119013997..119014002,+p@chr3:119013997..119014002
+
Hg19::chr3:5018897..5018920,-p@chr3:5018897..5018920
-
Hg19::chr3:5020060..5020082,-p@chr3:5020060..5020082
-
Hg19::chr3:5020146..5020171,+p@chr3:5020146..5020171
+
Hg19::chr4:103457066..103457069,+p@chr4:103457066..103457069
+
Hg19::chr4:107237802..107237819,+p@chr4:107237802..107237819
+
Hg19::chr4:107237829..107237840,+p@chr4:107237829..107237840
+
Hg19::chr5:100237813..100237824,-p@chr5:100237813..100237824
-
Hg19::chr5:133984176..133984203,-p@chr5:133984176..133984203
-
Hg19::chr6:143265842..143265868,+p@chr6:143265842..143265868
+
Hg19::chr6:150260042..150260087,-p@chr6:150260042..150260087
-
Hg19::chr6:44094627..44094662,+p3@TMEM63B
Hg19::chr7:104585602..104585616,-p@chr7:104585602..104585616
-
Hg19::chr7:104652294..104652297,-p@chr7:104652294..104652297
-
Hg19::chr7:105316500..105316514,+p@chr7:105316500..105316514
+
Hg19::chr7:48128459..48128476,-p@chr7:48128459..48128476
-
Hg19::chr8:141599124..141599145,+p@chr8:141599124..141599145
+
Hg19::chr9:123688609..123688619,+p@chr9:123688609..123688619
+
Hg19::chr9:128000415..128000420,-p@chr9:128000415..128000420
-
Hg19::chr9:5437979..5437984,+p@chr9:5437979..5437984
+


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:0004337geranyltranstransferase activity0.0141261637694952
GO:0004161dimethylallyltranstransferase activity0.0141261637694952
GO:0031616spindle pole centrosome0.0141261637694952
GO:0031229intrinsic to nuclear inner membrane0.0141261637694952
GO:0005639integral to nuclear inner membrane0.0141261637694952
GO:0004311farnesyltranstransferase activity0.0141261637694952
GO:0051298centrosome duplication0.0211845680019452
GO:0007098centrosome cycle0.0346376062360266
GO:0005637nuclear inner membrane0.0346376062360266
GO:0051297centrosome organization and biogenesis0.0346376062360266
GO:0031023microtubule organizing center organization and biogenesis0.0346376062360266
GO:0004659prenyltransferase activity0.0370348186593884



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
leukocyte2.68e-85136
classical monocyte8.11e-8242
CD14-positive, CD16-negative classical monocyte8.11e-8242
defensive cell5.60e-7048
phagocyte5.60e-7048
myeloid leukocyte2.70e-6972
hematopoietic stem cell2.81e-67168
angioblastic mesenchymal cell2.81e-67168
hematopoietic lineage restricted progenitor cell5.92e-67120
nongranular leukocyte7.79e-66115
hematopoietic cell1.04e-64177
granulocyte monocyte progenitor cell2.93e-6267
macrophage dendritic cell progenitor5.50e-6061
hematopoietic oligopotent progenitor cell1.14e-58161
hematopoietic multipotent progenitor cell1.14e-58161
myeloid lineage restricted progenitor cell1.58e-5766
monopoietic cell2.59e-5659
monocyte2.59e-5659
monoblast2.59e-5659
promonocyte2.59e-5659
myeloid cell3.16e-47108
common myeloid progenitor3.16e-47108
stuff accumulating cell9.94e-3587
mesenchymal cell2.22e-22354
connective tissue cell1.46e-21361
intermediate monocyte7.81e-199
CD14-positive, CD16-positive monocyte7.81e-199
motile cell1.12e-18386
stem cell1.35e-15441
multi fate stem cell3.66e-15427
somatic stem cell1.11e-14433
CD4-positive, alpha-beta T cell1.45e-136
mature alpha-beta T cell4.88e-1118
alpha-beta T cell4.88e-1118
immature T cell4.88e-1118
mature T cell4.88e-1118
immature alpha-beta T cell4.88e-1118
lymphoid lineage restricted progenitor cell6.08e-1152
lymphocyte1.22e-1053
common lymphoid progenitor1.22e-1053
granulocyte2.44e-108
nucleate cell4.49e-1055
blood cell1.66e-0911
natural killer cell1.42e-083
pro-NK cell1.42e-083
basophil2.35e-083
single nucleate cell8.04e-083
mononuclear cell8.04e-083
T cell2.55e-0725
pro-T cell2.55e-0725
naive T cell4.32e-073
plasmacytoid dendritic cell6.89e-073
Uber Anatomy
Ontology termp-valuen
bone marrow9.78e-5676
hematopoietic system5.87e-5198
blood island5.87e-5198
bone element1.16e-5082
immune system2.83e-4593
skeletal element6.00e-4590
hemolymphoid system7.36e-45108
skeletal system4.35e-39100
connective tissue1.92e-20371
musculoskeletal system4.80e-18167
lateral plate mesoderm4.81e-17203
mesoderm8.12e-07315
mesoderm-derived structure8.12e-07315
presumptive mesoderm8.12e-07315


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)
MA0003.11.19103
MA0004.10.763327
MA0006.10.405663
MA0007.10.988755
MA0009.10.517127
MA0014.10.109232
MA0017.10.547599
MA0019.10.038025
MA0024.10.754736
MA0025.10.259105
MA0027.11.6012
MA0028.10.9091
MA0029.10.127243
MA0030.10.121495
MA0031.10.0915635
MA0038.10.0272934
MA0040.10.407817
MA0041.10.328436
MA0042.10.26828
MA0043.10.517578
MA0046.10.167685
MA0048.10.131451
MA0050.11.01828
MA0051.11.16873
MA0052.10.412906
MA0055.10.0427309
MA0056.10
MA0057.10.702588
MA0058.11.5415
MA0059.10.642468
MA0060.10.103839
MA0061.12.19069
MA0063.10
MA0066.10.276234
MA0067.11.02386
MA0068.10.319989
MA0069.10.496197
MA0070.10.159116
MA0071.10.691207
MA0072.10.922928
MA0073.10.00183976
MA0074.10.801273
MA0076.10.714179
MA0077.10.152309
MA0078.10.431633
MA0081.10.899585
MA0083.10.527899
MA0084.10.550575
MA0087.10.470858
MA0088.10.316566
MA0089.10
MA0090.10.0835855
MA0091.10.14696
MA0092.10.230604
MA0093.10.83444
MA0095.10
MA0098.10
MA0100.10.545306
MA0101.13.38884
MA0103.10.235029
MA0105.11.2272
MA0106.10.146499
MA0107.13.96819
MA0108.20.0902489
MA0109.10
MA0111.10.204141
MA0113.10.041397
MA0114.10.451086
MA0115.10.336593
MA0116.10.0654435
MA0117.10.196603
MA0119.10.119757
MA0122.10.212824
MA0124.10.305891
MA0125.10.246933
MA0130.10
MA0131.10.806233
MA0132.10
MA0133.10
MA0135.10.192163
MA0136.12.67012
MA0139.10.01008
MA0140.10.417271
MA0141.10.258129
MA0142.10.0784053
MA0143.10.160626
MA0144.10.045511
MA0145.10.316603
MA0146.10.869904
MA0147.10.694562
MA0148.10.17213
MA0149.10.017743
MA0062.22.41754
MA0035.20.415727
MA0039.20.00736433
MA0138.20.195748
MA0002.20.637921
MA0137.20.313759
MA0104.20.915725
MA0047.20.136576
MA0112.20.452284
MA0065.20.815041
MA0150.11.36274
MA0151.10
MA0152.10.22632
MA0153.10.66414
MA0154.10.242447
MA0155.10.396109
MA0156.13.18734
MA0157.10.0679393
MA0158.10
MA0159.10.227059
MA0160.11.2806
MA0161.10
MA0162.10.317076
MA0163.10.324696
MA0164.10.0449147
MA0080.21.3975
MA0018.21.37963
MA0099.20.704806
MA0079.20.0272555
MA0102.20.582837
MA0258.10.672663
MA0259.10.24749
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
ATF3#46792.929979286001140.003459886809897840.0175820902364208
BATF#10538103.530116201783140.000500576618975510.00441179084465682
BCL11A#53335135.344969802128877.78734682833008e-073.41723830001666e-05
BHLHE40#855363.901896830171950.004421081584707160.0209421870294463
CEBPB#1051212.426001451337997.2620952890207e-050.0011415502256021
CTCF#10664231.786752124358340.002638113981790680.0145832840811008
E2F1#1869231.635796404959770.008155161400387650.0322022345455437
E2F4#1874132.38673600143040.002661923841356910.0146876935792199
E2F6#1876251.817810047716440.001213672086548960.00816876323046252
EBF1#1879283.614218430491773.90933375729495e-103.86635329808833e-08
EGR1#1958251.807311266235560.001322498807340150.00885047116107895
ELF1#1997342.098193197093572.75192663684192e-069.529458422584e-05
ELK4#2005133.058896544349050.0002701899502686620.00288472380046093
EP300#2033262.55249978089572.49064759389749e-068.77896537492609e-05
FOS#2353283.651344183319473.08733315870661e-103.11233578921003e-08
GATA1#2623193.733997894669693.80272468776927e-071.8602002982011e-05
GATA2#2624183.324764800057564.34737858923899e-060.0001362652678516
GATA3#262593.552589090070350.0009336924735302280.00676709980867616
HEY1#23462261.52236068290940.01169692738502120.0427018805636264
JUN#3725193.445561661657831.28287902208559e-065.12753931066196e-05
JUNB#372683.54905885910970.001833710439933230.0108535497101834
JUND#3727181.824694941357660.007161862100750310.0297418472281308
MAX#4149211.963821241871730.001339801479468540.00887583423496444
MEF2A#4205133.531333359788016.50117161038365e-050.00105611426631958
MEF2C#420874.191006977512590.001410684529980280.0091703275007227
MYC#4609241.816445868385880.001616258123115010.0101266052024722
NFKB1#4790372.94287458978514.02509809901318e-114.5892709646598e-09
NR3C1#2908122.604004057595310.001932706526537830.0113577502208578
PAX5#5079282.706490360477962.38113751652828e-071.24966643763164e-05
PBX3#509092.858414698270970.00406795865392320.0194574551800818
POLR2A#5430611.898473098116563.50287982970031e-135.17450164828954e-11
POU2F2#5452222.903401873483122.57629888629826e-069.0564146545306e-05
RAD21#5885152.25109432509920.002133102817068560.0123273088264621
REST#5978152.097832329593050.004195809344863610.0199847736657186
SIN3A#25942302.351689011658751.52938356902323e-065.86155194734741e-05
SMARCB1#659892.380789014933580.0128126164679720.0460981414943683
SMARCC1#659974.429616162861160.001027128930739080.00727664620794048
SMC3#9126112.398467554989290.005628901278100250.0254437057166636
SPI1#6688252.972580981348812.47925120131832e-071.29013710121816e-05
SRF#6722132.599468368234520.001245295201009280.00837405096247557
STAT3#6774203.049120289030214.11662223410668e-060.000130679607753151
TAF1#6872341.647298169787540.0005685007896298530.0048464332681538
TBP#6908371.987688629312552.55545666710079e-068.98919969199526e-05
TCF12#6938162.465962875869320.000553963844172540.00472945556458235
TCF7L2#6934162.49743224652460.0004817039444533670.00438419854072028
TFAP2A#7020122.872805977920860.0008346481064406040.0062974868941302
USF2#7392152.824390735884690.0002029817813352380.00241037114961579
WRNIP1#5689746.366374744891370.003703875293557920.0186837824470583
YY1#7528261.850586079655080.0006916200882168230.00557518604455671
ZNF263#10127192.263985378307290.0004374597961148270.00407745324823172



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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