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{{Coexpression_clusters
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105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.00147244,0.15113,8.4053e-05,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.000168983,0.0192232,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.00335066,0.177664,0.28365,0.0385243,0.131761,0.160658,0.206239,0.19924,1.55457e-06,0.236464,0.325148,0.115817,0.00206474,0.223831,0.11528,3.33991e-06,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,2.62123,0.853988,2.1595,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,1.53533,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.427404,0.596053,0.855276,1.39264,0.469078,2.48207,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,1.55608,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,2.13568,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,2.54768,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,3.03565,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;2.94911,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;2.86846,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;3.21605,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;1.98824,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;1.76247,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0107199,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3231_lymphangiectasia_Whole_CD4_Neutrophils_CD14_Eosinophils_migratory
|id=C3231
}}

Latest revision as of 12:21, 17 September 2013


Full id: C3231_lymphangiectasia_Whole_CD4_Neutrophils_CD14_Eosinophils_migratory



Phase1 CAGE Peaks

Hg19::chr12:109027545..109027622,-p1@SELPLG
Hg19::chr12:109027626..109027638,-p3@SELPLG
Hg19::chr12:109027643..109027677,-p2@SELPLG


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
hematopoietic stem cell8.51e-79168
angioblastic mesenchymal cell8.51e-79168
hematopoietic oligopotent progenitor cell9.32e-76161
hematopoietic multipotent progenitor cell9.32e-76161
hematopoietic cell1.01e-72177
leukocyte4.48e-67136
hematopoietic lineage restricted progenitor cell1.80e-56120
nongranular leukocyte1.25e-54115
myeloid cell1.34e-53108
common myeloid progenitor1.34e-53108
myeloid leukocyte2.26e-4272
granulocyte monocyte progenitor cell1.35e-3667
myeloid lineage restricted progenitor cell2.61e-3666
macrophage dendritic cell progenitor8.04e-3461
monopoietic cell2.47e-3359
monocyte2.47e-3359
monoblast2.47e-3359
promonocyte2.47e-3359
defensive cell6.14e-3148
phagocyte6.14e-3148
classical monocyte6.31e-2742
CD14-positive, CD16-negative classical monocyte6.31e-2742
nucleate cell9.21e-1955
lymphoid lineage restricted progenitor cell1.92e-1852
lymphocyte1.99e-1853
common lymphoid progenitor1.99e-1853
T cell2.33e-1525
pro-T cell2.33e-1525
mature alpha-beta T cell2.10e-1218
alpha-beta T cell2.10e-1218
immature T cell2.10e-1218
mature T cell2.10e-1218
immature alpha-beta T cell2.10e-1218
mesenchymal cell2.62e-11354
connective tissue cell3.49e-10361
stuff accumulating cell2.36e-0987
CD8-positive, alpha-beta T cell2.85e-0811
intermediate monocyte8.82e-089
CD14-positive, CD16-positive monocyte8.82e-089
granulocyte1.77e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.00e-4398
blood island3.00e-4398
hemolymphoid system5.07e-38108
bone marrow7.61e-3176
immune system9.75e-3093
adult organism1.39e-29114
bone element1.30e-2882
skeletal element2.21e-2390
skeletal system1.74e-19100
neural tube2.17e-1056
neural rod2.17e-1056
future spinal cord2.17e-1056
neural keel2.17e-1056
regional part of nervous system2.25e-0953
regional part of brain2.25e-0953
blood3.41e-0915
haemolymphatic fluid3.41e-0915
organism substance3.41e-0915
lateral plate mesoderm4.42e-09203
regional part of forebrain4.81e-0941
forebrain4.81e-0941
anterior neural tube4.81e-0941
future forebrain4.81e-0941
connective tissue5.43e-09371
telencephalon1.13e-0734
brain grey matter1.93e-0734
gray matter1.93e-0734
regional part of telencephalon6.01e-0732
cerebral hemisphere7.81e-0732
Disease
Ontology termp-valuen
leukemia3.09e-1239
hematologic cancer1.07e-1151
immune system cancer1.07e-1151
myeloid leukemia3.38e-1031


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.12.94911
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.12.86846
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCL11A#53335328.36945510360714.37778126761649e-050.000776777264370707
BCL3#602334.54710280373832.42397750207122e-050.000526534497376906
CHD2#1106310.34402283411690.0009033701102746880.0065875625573927
CTCF#1066435.360256373075030.0064925092527670.0278537287976394
EBF1#187938.9064668465690.00141523283560980.00912774051245923
EGR1#195834.988179094810140.008056488137383440.0319321276880527
ELF1#199734.258097958807540.01295179875054610.0460390357614881
GATA1#2623313.56030814380040.0004009615963782630.00387024289871991
IRF4#3662321.91451268674419.49854535978121e-050.00136210157741342
MAX#414936.452555509007120.003721913834265510.018591589771229
MYC#460935.22228187160940.007020843755740150.0293405586413407
NFKB1#479035.488063424193840.006049381815655430.0268755907540088
PAX5#507936.669565531177830.003370290999677260.0172434145747952
POU2F2#545239.106124057742520.001324165192682130.00879959840662566
SP1#666735.69838137814090.005403962701712170.0245619488469021
SPI1#668838.204323508522730.001810593189410520.0108845071149971
SRF#6722313.79717826216780.0003806615025800190.00374067620135064
TCF12#6938310.63446490218640.0008313523990202070.00627987944461676
USF1#739136.361499277207960.00388404057290560.0189651369112015
USF2#7392312.99219738506960.0004558979393427810.0042061417744718
YY1#752834.911170749853860.008441455341808260.0328177916335286
ZEB1#6935316.88843201754390.0002075486917327580.00242164873375908



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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