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Coexpression cluster:C677: Difference between revisions

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{{Coexpression_clusters
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0.431728,0.503688,0.603029,0.588841,0.155138,0.660126,0.466319,0.38882,0.626139,0.637069,0.387334,0.580026,0.571641,0.73383,0.736033,0.683517,0.513034,0.637864,0.324971,0.795613,0.640649,0.606125,0.33179,0.301892,0.782217,0.529255,0.49939,0.717997,0.255516,0.716956,0.346873,0.634662,0.538845,0.495634,0.621629,0.688286,0.602459,0.833727|tfbs_overrepresentation_for_novel_motifs=0.649083,0.607441,0.223258,0.913546,0.190185,0.344001,0.411652,0.340819,0.687431,0.149656,0.317729,0.451026,0.0765797,0.401301,0.189126,1.12766,1.49799,0.455132,0.0839658,0.848367,0.635173,0.356848,0.337221,0.18624,0.260754,0.471832,0.231222,1.59978,0.192587,0.790468,0.809412,0.65246,0.790946,1.43308,0.953152,0.225495,0.161511,0.345014,1.40365,0.306232,0.48973,0.285097,0.658594,0.550978,0.437801,0.24831,0.412635,0.308385,0.369629,0.192687,1.21719,0.423285,0.150575,0.725869,0.873575,1.04226,1.70369,0.374657,0.454008,0.373762,0.691524,0.414771,0.103208,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,0.350755,0.0373297,0.871629,0.257259,0.237079,2.28612,0.575479,0.639503,0.255642,1.52117,0.590372,0.4307,0.703506,0.821696,0.180819,0.285494,0.76968,0.508983,1.42111,2.39034,0.795567,0.66846,0.409242,0.190761,0.432898,0.0830795,0.709167,0.51326,2.5969,0.145361,0.663075,0.703825,0.621018,1.35204,0.313822,0.606045,0.398205,0.721801,0.52669,0.656353,0.701175,0.21882,2.37773,1.00416,0.16034,0.00677971,0.297931,0.556847,0.132787,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,1.8449,0.673222,0.905059,0.434621,0.796235,0.301402,0.919079,0.437919,1.06395,1.13627,0.797863,0.892152,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.128495,0.57206,0.0163338,0.796604,1.62429,0.414334,1.19239,1.23664,1.61037,0.260802,0.237047,0.984474,0.778717,0.638755,0.239672,0.564971,1.09889,0.120139,0.410452,0.51183|tfbs_overrepresentation_jaspar=MA0003.1;0.0958548,MA0004.1;0.32225,MA0006.1;2.36084,MA0007.1;0.305951,MA0009.1;0.756202,MA0014.1;0.00141144,MA0017.1;0.220105,MA0019.1;0.45566,MA0024.1;1.57618,MA0025.1;0.886436,MA0027.1;2.35633,MA0028.1;1.10416,MA0029.1;0.673506,MA0030.1;0.662482,MA0031.1;0.600685,MA0038.1;0.414169,MA0040.1;0.67914,MA0041.1;0.338572,MA0042.1;0.310552,MA0043.1;1.78706,MA0046.1;0.745626,MA0048.1;1.4241,MA0050.1;0.311321,MA0051.1;1.05617,MA0052.1;0.682867,MA0055.1;7.75336,MA0056.1;0,MA0057.1;0.147728,MA0058.1;0.240796,MA0059.1;0.239727,MA0060.1;0.103131,MA0061.1;0.28989,MA0063.1;0,MA0066.1;0.414559,MA0067.1;2.42329,MA0068.1;0.0633085,MA0069.1;0.741884,MA0070.1;0.731026,MA0071.1;0.379038,MA0072.1;0.726666,MA0073.1;0.00573911,MA0074.1;0.40963,MA0076.1;0.706813,MA0077.1;0.719193,MA0078.1;0.502027,MA0081.1;0.239862,MA0083.1;0.763502,MA0084.1;1.25286,MA0087.1;0.724294,MA0088.1;0.0806254,MA0089.1;0,MA0090.1;0.266215,MA0091.1;0.324543,MA0092.1;0.291716,MA0093.1;0.191154,MA0095.1;0,MA0098.1;0,MA0100.1;1.09213,MA0101.1;0.19375,MA0103.1;0.181541,MA0105.1;0.307721,MA0106.1;1.14663,MA0107.1;0.137948,MA0108.2;0.597764,MA0109.1;0,MA0111.1;0.277713,MA0113.1;0.467266,MA0114.1;0.828144,MA0115.1;0.992167,MA0116.1;0.854781,MA0117.1;0.792789,MA0119.1;1.87032,MA0122.1;0.818044,MA0124.1;0.951337,MA0125.1;0.868909,MA0130.1;0,MA0131.1;0.519055,MA0132.1;0,MA0133.1;0,MA0135.1;0.785738,MA0136.1;0.420617,MA0139.1;0.268952,MA0140.1;0.376643,MA0141.1;2.7101,MA0142.1;0.570448,MA0143.1;0.467429,MA0144.1;0.124153,MA0145.1;1.05522,MA0146.1;0.246584,MA0147.1;0.143012,MA0148.1;0.910784,MA0149.1;0.367947,MA0062.2;0.589182,MA0035.2;0.376007,MA0039.2;0.000717146,MA0138.2;0.503176,MA0002.2;0.316618,MA0137.2;0.20663,MA0104.2;0.102626,MA0047.2;0.440861,MA0112.2;0.416057,MA0065.2;1.92393,MA0150.1;2.86453,MA0151.1;0,MA0152.1;0.382565,MA0153.1;0.852412,MA0154.1;0.875403,MA0155.1;0.0793743,MA0156.1;0.600064,MA0157.1;0.544523,MA0158.1;0,MA0159.1;0.143477,MA0160.1;0.940794,MA0161.1;0,MA0162.1;0.260011,MA0163.1;0.478611,MA0164.1;0.478818,MA0080.2;0.558855,MA0018.2;1.14938,MA0099.2;0.996203,MA0079.2;4.82454e-06,MA0102.2;1.28978,MA0258.1;0.375,MA0259.1;0.149181,MA0442.1;0}}
|full_id=C677_Basophils_CD14_Eosinophils_Neutrophils_CD34_Peripheral_immature
|id=C677
|ontology_enrichment_celltype=CL:0000037!3.63e-50!172;CL:0000566!3.63e-50!172;CL:0000738!3.81e-49!140;CL:0000988!2.28e-47!182;CL:0002032!2.08e-45!165;CL:0000837!2.08e-45!165;CL:0002031!1.90e-37!124;CL:0002087!2.55e-36!119;CL:0000763!7.41e-34!112;CL:0000049!7.41e-34!112;CL:0002057!6.91e-33!42;CL:0000766!4.29e-32!76;CL:0000860!4.16e-31!45;CL:0000557!4.29e-28!71;CL:0002009!4.22e-26!65;CL:0000839!1.75e-25!70;CL:0002194!1.07e-24!63;CL:0000576!1.07e-24!63;CL:0000040!1.07e-24!63;CL:0000559!1.07e-24!63;CL:0000134!1.31e-16!358;CL:0002320!1.47e-15!365;CL:0000219!1.58e-13!390;CL:0000838!8.78e-11!52;CL:0000542!2.62e-10!53;CL:0000051!2.62e-10!53;CL:0000048!4.31e-09!430;CL:0000034!1.18e-08!444;CL:0000723!2.76e-08!436;CL:0000094!9.45e-08!8;CL:0002393!3.94e-07!9;CL:0002397!3.94e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.35e-32!102;UBERON:0003061!1.35e-32!102;UBERON:0002193!1.29e-27!112;UBERON:0002371!1.25e-25!80;UBERON:0001474!2.36e-23!86;UBERON:0002405!4.85e-17!115;UBERON:0004765!7.40e-17!101;UBERON:0001434!7.40e-17!101;UBERON:0002384!4.21e-15!375;UBERON:0003081!1.64e-08!216;UBERON:0000178!1.42e-07!15;UBERON:0000179!1.42e-07!15;UBERON:0000463!1.42e-07!15
}}

Latest revision as of 11:28, 17 September 2013


Full id: C677_Basophils_CD14_Eosinophils_Neutrophils_CD34_Peripheral_immature



Phase1 CAGE Peaks

Hg19::chr10:81034106..81034115,-p@chr10:81034106..81034115
-
Hg19::chr10:81046025..81046036,-p@chr10:81046025..81046036
-
Hg19::chr10:81046046..81046068,-p@chr10:81046046..81046068
-
Hg19::chr10:81046489..81046500,+p@chr10:81046489..81046500
+
Hg19::chr10:81046514..81046556,+p@chr10:81046514..81046556
+
Hg19::chr10:81046677..81046703,+p@chr10:81046677..81046703
+
Hg19::chr17:78844208..78844221,-p@chr17:78844208..78844221
-
Hg19::chr19:6062269..6062283,-p@chr19:6062269..6062283
-
Hg19::chr19:6062285..6062295,-p@chr19:6062285..6062295
-
Hg19::chr19:6062297..6062310,-p@chr19:6062297..6062310
-
Hg19::chr3:156809021..156809030,-p@chr3:156809021..156809030
-
Hg19::chr6:170862436..170862458,+p@chr6:170862436..170862458
+


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 monocyte3.93e-10542
CD14-positive, CD16-negative classical monocyte3.93e-10542
defensive cell8.46e-9148
phagocyte8.46e-9148
myeloid leukocyte6.22e-8772
granulocyte monocyte progenitor cell2.38e-8067
macrophage dendritic cell progenitor2.84e-7661
myeloid lineage restricted progenitor cell1.46e-7366
monopoietic cell9.88e-7159
monocyte9.88e-7159
monoblast9.88e-7159
promonocyte9.88e-7159
leukocyte1.22e-67136
myeloid cell2.89e-60108
common myeloid progenitor2.89e-60108
hematopoietic stem cell8.98e-55168
angioblastic mesenchymal cell8.98e-55168
hematopoietic cell2.10e-51177
hematopoietic lineage restricted progenitor cell9.42e-50120
nongranular leukocyte2.68e-47115
stuff accumulating cell7.94e-4687
hematopoietic oligopotent progenitor cell1.29e-44161
hematopoietic multipotent progenitor cell1.29e-44161
mesenchymal cell7.72e-21354
connective tissue cell3.35e-20361
motile cell5.95e-18386
stem cell3.97e-16441
multi fate stem cell3.36e-15427
somatic stem cell8.07e-15433
intermediate monocyte3.53e-139
CD14-positive, CD16-positive monocyte3.53e-139
basophil5.13e-123
granulocyte2.87e-118
single nucleate cell1.59e-103
mononuclear cell1.59e-103
natural killer cell2.98e-103
pro-NK cell2.98e-103
blood cell4.37e-0811
CD1a-positive Langerhans cell9.23e-082
immature CD1a-positive Langerhans cell9.23e-082
somatic cell1.42e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow2.94e-7376
bone element3.34e-6782
hematopoietic system2.05e-6398
blood island2.05e-6398
skeletal element2.26e-6090
immune system4.14e-5893
hemolymphoid system1.35e-56108
skeletal system2.36e-53100
musculoskeletal system6.76e-28167
lateral plate mesoderm1.52e-26203
connective tissue2.49e-19371
mesoderm2.97e-13315
mesoderm-derived structure2.97e-13315
presumptive mesoderm2.97e-13315


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)
MA0003.10.0958548
MA0004.10.32225
MA0006.12.36084
MA0007.10.305951
MA0009.10.756202
MA0014.10.00141144
MA0017.10.220105
MA0019.10.45566
MA0024.11.57618
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
MA0043.11.78706
MA0046.10.745626
MA0048.11.4241
MA0050.10.311321
MA0051.11.05617
MA0052.10.682867
MA0055.17.75336
MA0056.10
MA0057.10.147728
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.28989
MA0063.10
MA0066.10.414559
MA0067.12.42329
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.00573911
MA0074.10.40963
MA0076.10.706813
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0806254
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.11.09213
MA0101.10.19375
MA0103.10.181541
MA0105.10.307721
MA0106.11.14663
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.828144
MA0115.10.992167
MA0116.10.854781
MA0117.10.792789
MA0119.11.87032
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.268952
MA0140.10.376643
MA0141.12.7101
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.11.05522
MA0146.10.246584
MA0147.10.143012
MA0148.10.910784
MA0149.10.367947
MA0062.20.589182
MA0035.20.376007
MA0039.20.000717146
MA0138.20.503176
MA0002.20.316618
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.20.416057
MA0065.21.92393
MA0150.12.86453
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.875403
MA0155.10.0793743
MA0156.10.600064
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.940794
MA0161.10
MA0162.10.260011
MA0163.10.478611
MA0164.10.478818
MA0080.20.558855
MA0018.21.14938
MA0099.20.996203
MA0079.24.82454e-06
MA0102.21.28978
MA0258.10.375
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
BATF#1053848.119267264101210.001077324937599460.00760748743461459
BCL11A#5333549.456485034535690.0006080261876137550.00507485391258635
BCL3#602514.39462616822431.35480146970731e-050.000328368787873665
CHD2#110654.310009514215360.00373109116758340.0185947428159593
EBF1#187953.711027852737090.007149884520589760.0297240183681981
ELF1#199772.483890475971060.009986512778965350.0374566855134624
EP300#203363.38697086311160.004274673782939630.0203103887546714
FOSL1#8061413.23785990545770.0001689953220740490.00206550057836064
GATA2#262444.248310577851330.01122661586864120.0412197762244688
IRF4#366259.131046952810050.0001194522965794710.00162103409595418
MAX#4149105.377129590839273.88944661088221e-071.89198842381894e-05
MEF2A#420546.247743636548020.002834712427412020.0153706729248992
MEF2C#4208413.77045149754130.0001452363397035950.00188684389629354
POU2F2#545253.794218357392720.006499616292676570.0278339111854538
REST#597864.825014358064010.000656447359345280.00537420285040854
RXRA#625646.691539046377760.002204954724098080.0127031810696204
SPI1#668864.102161754261360.001568896548030080.00994923714735037
TCF12#693865.317232451093210.0003865425927634440.00378209873015002
ZBTB33#10009513.19363542915882.06208457123933e-050.000456082275594376



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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