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Coexpression cluster:C590: Difference between revisions

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{{Coexpression_clusters
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cell surface interactions (Reactome):REACT_13552!1.95641411763581e-05;0.00619205068231735;4;511;Signaling in Immune system 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,0.0469897,0.0606376,0.032823,0.438989,0.201933,0.292836,0.374626,0.170712,0.515655,0.681219,0.523107,0.503394,0.358777,0.0424111,0.782795,0.771969,0.672536,0.369827,0.829964,0.768195,0.256159,0.811363,0.200099,0.506604,0.218634,0.006632,0.304985,0.091788,0.390427,0.136849,0.459605,0.127047,0.361416,0.00360957,0.295275,0.653454,0.230823,0.49578,0.0158112,0.593207,0.719076,0.087562,0.58983,0.138152,0.112939,0.395855,0.361878,0.851225,0.242842,0.214706,0.0227192,0.0533953,0.0757688,0.412853,0.715967,0.252297,0.574957,0.123749,0.0603722,0.320349,0.0771899|tfbs_overrepresentation_for_novel_motifs=0.172755,2.63675,0.501231,0.277483,0.429786,0.276158,0.338925,0.241,0.237344,0.315942,0.702309,0.3759,0.707389,0.329255,0.137951,0.467196,0.534852,0.104074,0.431744,0.587627,0.16756,0.596488,0.26993,0.42122,0.581509,0.395548,0.627513,0.739386,0.856732,0.568017,0.235027,0.568576,0.0851517,0.180835,0.37247,1.17198,0.114552,0.759737,0.100329,0.212026,0.745946,0.222502,0.667607,0.136946,1.64248,0.189598,0.901103,0.682582,0.394038,0.435216,0.407934,0.349819,0.698571,0.639823,0.784252,0.882989,0.143846,0.821863,0.896459,0.303639,0.606437,0.341844,0.238061,0.509653,0.939336,0.478604,0.869007,1.22829,0.559029,1.06908,0.212516,0.249409,0.420444,0.782342,1.50973,0.155706,0.325762,0.494371,0.556046,0.196113,0.774709,0.50868,0.356776,0.245133,0.733386,0.682239,0.0669348,0.126142,0.430803,1.32629,0.95934,1.68624,0.584068,0.0892066,0.139351,0.658841,0.427968,0.623577,1.10949,0.789337,0.33179,0.578851,0.618385,0.538198,0.468285,0.248535,0.523764,0.326366,0.581061,0.403142,0.175484,0.61581,0.163638,0.259545,0.912801,0.364707,1.08286,0.660476,0.476505,0.0908333,0.77444,0.428661,0.273941,0.366411,1.02031,1.23889,0.33358,0.588683,0.815183,0.0973529,0.708473,0.667822,0.828971,0.363559,0.971853,0.525168,0.651842,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,1.50374,0.469857,0.297516,0.454976,1.61933,0.219968,0.61354,2.18296,1.23015,0.708834,0.844164,0.341434,1.09904,1.06976,0.406462,0.581613,1.01735,0.893382,0.691354,0.555323,0.181952,0.48429,0.356103,0.979783,0.337803,2.92229|tfbs_overrepresentation_jaspar=MA0003.1;5.93609,MA0004.1;0.711841,MA0006.1;0.426713,MA0007.1;0.241375,MA0009.1;0.669377,MA0014.1;2.52279,MA0017.1;0.494446,MA0019.1;0.38027,MA0024.1;0.570967,MA0025.1;0.796882,MA0027.1;2.25966,MA0028.1;0.454219,MA0029.1;0.588958,MA0030.1;0.578277,MA0031.1;0.518602,MA0038.1;0.34128,MA0040.1;0.594421,MA0041.1;0.27117,MA0042.1;0.245557,MA0043.1;0.669676,MA0046.1;0.659066,MA0048.1;0.717599,MA0050.1;0.246257,MA0051.1;0.337676,MA0052.1;0.598036,MA0055.1;0.579321,MA0056.1;0,MA0057.1;0.420982,MA0058.1;0.182945,MA0059.1;0.182001,MA0060.1;0.237888,MA0061.1;1.17249,MA0063.1;0,MA0066.1;0.905108,MA0067.1;0.975379,MA0068.1;0.147451,MA0069.1;0.655419,MA0070.1;0.644843,MA0071.1;0.308534,MA0072.1;0.640598,MA0073.1;1.26712,MA0074.1;0.337035,MA0076.1;0.194691,MA0077.1;0.633326,MA0078.1;0.424186,MA0081.1;0.536866,MA0083.1;0.676499,MA0084.1;1.15904,MA0087.1;0.63829,MA0088.1;1.66006,MA0089.1;0,MA0090.1;0.205547,MA0091.1;0.716673,MA0092.1;0.228476,MA0093.1;0.431889,MA0095.1;0,MA0098.1;0,MA0100.1;0.353174,MA0101.1;0.437519,MA0103.1;0.131472,MA0105.1;3.19108,MA0106.1;0.37688,MA0107.1;0.315431,MA0108.2;0.515791,MA0109.1;0,MA0111.1;0.215855,MA0113.1;1.01449,MA0114.1;0.636237,MA0115.1;0.900969,MA0116.1;2.20924,MA0117.1;0.705104,MA0119.1;0.97973,MA0122.1;0.729811,MA0124.1;0.860724,MA0125.1;0.779672,MA0130.1;0,MA0131.1;0.440395,MA0132.1;0,MA0133.1;0,MA0135.1;0.698212,MA0136.1;0.347318,MA0139.1;0.406749,MA0140.1;0.30631,MA0141.1;0.180729,MA0142.1;0.489543,MA0143.1;0.391385,MA0144.1;0.284854,MA0145.1;1.04117,MA0146.1;1.94265,MA0147.1;0.326612,MA0148.1;0.276339,MA0149.1;3.10598,MA0062.2;0.191053,MA0035.2;0.305721,MA0039.2;1.80801,MA0138.2;0.425279,MA0002.2;1.25767,MA0137.2;0.153033,MA0104.2;0.236755,MA0047.2;0.366327,MA0112.2;0.692762,MA0065.2;1.42425,MA0150.1;0.201098,MA0151.1;0,MA0152.1;0.311809,MA0153.1;0.763487,MA0154.1;3.15079,MA0155.1;3.00188,MA0156.1;0.469333,MA0157.1;0.46471,MA0158.1;0,MA0159.1;0.671959,MA0160.1;0.288813,MA0161.1;0,MA0162.1;0.234575,MA0163.1;3.8716,MA0164.1;0.402162,MA0080.2;0.851709,MA0018.2;0.378086,MA0099.2;0.312108,MA0079.2;5.68149,MA0102.2;1.1957,MA0258.1;0.27007,MA0259.1;0.693919,MA0442.1;0}}
|full_id=C590_CD4_CD14CD16_CD14_CD19_Neutrophils_Whole_blood
|id=C590
}}

Latest revision as of 11:26, 17 September 2013


Full id: C590_CD4_CD14CD16_CD14_CD19_Neutrophils_Whole_blood



Phase1 CAGE Peaks

Hg19::chr11:64511549..64511566,-p5@RASGRP2
Hg19::chr12:51717831..51717874,-p3@BIN2
Hg19::chr14:100531713..100531724,+p11@EVL
Hg19::chr15:75074868..75074911,+p2@CSK
Hg19::chr15:75074915..75074938,+p5@CSK
Hg19::chr16:30194916..30194955,+p1@CORO1A
Hg19::chr16:30198468..30198483,+p3@CORO1A
Hg19::chr17:61775799..61775815,-p@chr17:61775799..61775815
-
Hg19::chr17:61776662..61776738,-p2@LIMD2
Hg19::chr17:62097927..62098000,-p1@ICAM2
Hg19::chr19:3178814..3178835,+p2@S1PR4
Hg19::chr19:49838937..49838974,+p@chr19:49838937..49838974
+
Hg19::chr1:167599532..167599568,+p3@RCSD1
Hg19::chr4:83196097..83196106,+p1@ENST00000504996
Hg19::chr7:77428066..77428132,+p2@PHTF2


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

p.valueFDRnGenesnPathwayName
3.01170464246961e-060.00190640903868326385Integrin cell surface interactions (Reactome):REACT_13552
1.95641411763581e-050.006192050682317354511Signaling in Immune system (Reactome):REACT_6900



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 cell6.59e-97168
angioblastic mesenchymal cell6.59e-97168
hematopoietic cell5.05e-93177
hematopoietic oligopotent progenitor cell6.12e-91161
hematopoietic multipotent progenitor cell6.12e-91161
leukocyte3.56e-89136
nongranular leukocyte8.76e-80115
hematopoietic lineage restricted progenitor cell2.52e-75120
myeloid cell8.38e-47108
common myeloid progenitor8.38e-47108
myeloid leukocyte4.77e-4272
nucleate cell8.34e-4055
lymphocyte2.13e-3953
common lymphoid progenitor2.13e-3953
lymphoid lineage restricted progenitor cell1.10e-3852
myeloid lineage restricted progenitor cell7.11e-3666
monopoietic cell8.65e-3559
monocyte8.65e-3559
monoblast8.65e-3559
promonocyte8.65e-3559
granulocyte monocyte progenitor cell3.01e-3467
macrophage dendritic cell progenitor6.07e-3361
defensive cell2.45e-3248
phagocyte2.45e-3248
classical monocyte1.03e-2942
CD14-positive, CD16-negative classical monocyte1.03e-2942
lymphocyte of B lineage1.22e-1924
pro-B cell1.22e-1924
mesenchymal cell1.32e-18354
T cell1.00e-1725
pro-T cell1.00e-1725
connective tissue cell2.25e-17361
mature alpha-beta T cell5.49e-1618
alpha-beta T cell5.49e-1618
immature T cell5.49e-1618
mature T cell5.49e-1618
immature alpha-beta T cell5.49e-1618
B cell9.23e-1414
motile cell3.64e-13386
CD8-positive, alpha-beta T cell1.04e-1011
stuff accumulating cell2.79e-1087
intermediate monocyte1.44e-099
CD14-positive, CD16-positive monocyte1.44e-099
multi fate stem cell5.63e-09427
stem cell1.44e-08441
somatic stem cell2.43e-08433
granulocyte5.56e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.73e-4698
blood island7.73e-4698
hemolymphoid system1.77e-41108
immune system2.76e-3093
bone marrow7.69e-3076
bone element5.49e-2682
skeletal element1.04e-2190
skeletal system4.71e-18100
connective tissue3.69e-16371
blood8.05e-1315
haemolymphatic fluid8.05e-1315
organism substance8.05e-1315
lateral plate mesoderm2.72e-10203
Disease
Ontology termp-valuen
hematologic cancer6.16e-1451
immune system cancer6.16e-1451
leukemia9.12e-1139
myeloid leukemia2.60e-0731


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)
MA0003.15.93609
MA0004.10.711841
MA0006.10.426713
MA0007.10.241375
MA0009.10.669377
MA0014.12.52279
MA0017.10.494446
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.717599
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.579321
MA0056.10
MA0057.10.420982
MA0058.10.182945
MA0059.10.182001
MA0060.10.237888
MA0061.11.17249
MA0063.10
MA0066.10.905108
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.11.26712
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.11.66006
MA0089.10
MA0090.10.205547
MA0091.10.716673
MA0092.10.228476
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.437519
MA0103.10.131472
MA0105.13.19108
MA0106.10.37688
MA0107.10.315431
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.11.01449
MA0114.10.636237
MA0115.10.900969
MA0116.12.20924
MA0117.10.705104
MA0119.10.97973
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.406749
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.11.04117
MA0146.11.94265
MA0147.10.326612
MA0148.10.276339
MA0149.13.10598
MA0062.20.191053
MA0035.20.305721
MA0039.21.80801
MA0138.20.425279
MA0002.21.25767
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.20.692762
MA0065.21.42425
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.13.15079
MA0155.13.00188
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.671959
MA0160.10.288813
MA0161.10
MA0162.10.234575
MA0163.13.8716
MA0164.10.402162
MA0080.20.851709
MA0018.20.378086
MA0099.20.312108
MA0079.25.68149
MA0102.21.1957
MA0258.10.27007
MA0259.10.693919
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
EBF1#187984.750115651503477.80369455890836e-050.00120243442909093
ELF1#199782.270985578030690.01178598236921460.0429414342458889
NFKB1#479093.29283805451630.0003804048935776930.00376579210240385
POLR2A#5430142.00428963145420.0001911089001665770.00230662457234453
SPI1#668873.828684303977270.001049613452727730.00741882643404382
ZEB1#693544.503581871345030.009893096304177240.0371183030935468



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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