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Coexpression cluster:C728: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.253158,0.306045,0.246925,0.373402,0.21227,0.371921,0.44126,0.121034,1.24596,0.185549,0.344881,0.481459,0.0905352,0.430675,0.606477,0.651838,0.650562,0.168654,3.59587,0.14663,0.246975,1.84095,0.36495,0.20812,0.28596,0.50266,0.0775775,0.952441,0.214796,0.24094,0.869128,1.64064,0.14393,0.0919867,0.542692,0.00368855,0.182011,0.372963,0.163827,0.107051,0.540033,0.836994,0.101961,0.209923,1.40347,0.273032,1.12547,0.89086,0.0920755,0.214901,0.515974,0.453148,1.54965,0.760015,0.908824,0.433372,1.16995,0.40339,2.42727,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,0.125091,0.0464399,0.906867,0.0876634,0.0798316,0.536377,0.607953,0.672773,0.767864,0.101808,0.623044,1.16527,0.123028,0.856604,0.00700967,0.0364455,0.233,0.540459,1.45821,1.08742,0.830286,1.67425,0.456075,0.610551,0.480816,0.663027,0.743159,1.34473,0.792069,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.256397,0.735091,0.679564,0.353283,1.04009,0.533593,0.47353,0.324453,0.58906,0.151445,0.898765,0.538171,0.369441,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,0.468088,1.10012,0.222005,0.32024,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,0.566218,1.75262,0.308276,0.146851,1.01851,0.0945004,0.831331,0.113748,0.444001,1.22899,0.525224,0.200973,0.286011,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,0.459987,0.137885,0.440034,4.63739
|tfbs_overrepresentation_jaspar=MA0003.1;0.138892,MA0004.1;0.349539,MA0006.1;0.210781,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.114225,MA0017.1;1.9612,MA0019.1;0.486183,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.224112,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;0.443833,MA0040.1;0.712837,MA0041.1;0.366339,MA0042.1;0.337481,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;0.0494179,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;0.0496191,MA0056.1;0,MA0057.1;0.0465155,MA0058.1;0.265212,MA0059.1;0.2641,MA0060.1;0.38025,MA0061.1;0.100525,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;0.556338,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;0.760818,MA0073.1;0.000309691,MA0074.1;0.439193,MA0076.1;0.278993,MA0077.1;0.753278,MA0078.1;0.533387,MA0081.1;0.26424,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.10094,MA0089.1;0,MA0090.1;0.792817,MA0091.1;0.351901,MA0092.1;1.53836,MA0093.1;0.213288,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;1.16085,MA0103.1;0.587485,MA0105.1;0.645738,MA0106.1;0.482519,MA0107.1;0.156959,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.303543,MA0113.1;0.498009,MA0114.1;2.0906,MA0115.1;1.02805,MA0116.1;0.935607,MA0117.1;1.93331,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.0922451,MA0140.1;0.405425,MA0141.1;0.2626,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.142196,MA0145.1;0.515404,MA0146.1;3.16699,MA0147.1;0.162359,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;1.04409,MA0039.2;0.00623756,MA0138.2;0.534556,MA0002.2;0.725804,MA0137.2;0.229531,MA0104.2;0.118985,MA0047.2;0.47109,MA0112.2;2.02459,MA0065.2;2.13353,MA0150.1;1.4246,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.989789,MA0155.1;0.245306,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.948902,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.0809571,MA0163.1;0.387319,MA0164.1;0.509774,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;2.78803,MA0079.2;0.0134506,MA0102.2;1.32663,MA0258.1;0.135061,MA0259.1;0.168926,MA0442.1;0
}}
}}

Revision as of 19:24, 22 January 2013


Full id: C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute



Phase1 CAGE Peaks

Hg19::chr10:80732616..80732631,+p@chr10:80732616..80732631
+
Hg19::chr10:80732642..80732657,+p@chr10:80732642..80732657
+
Hg19::chr10:80732663..80732675,+p@chr10:80732663..80732675
+
Hg19::chr14:35837883..35837893,-p@chr14:35837883..35837893
-
Hg19::chr16:28995941..28995949,-p5@CU678918
Hg19::chr16:28995973..28995989,-p2@CU678918
Hg19::chr18:2894355..2894361,-p@chr18:2894355..2894361
-
Hg19::chr2:63605711..63605712,+p@chr2:63605711..63605712
+
Hg19::chr4:158234555..158234556,+p@chr4:158234555..158234556
+
Hg19::chr4:87928626..87928670,-p@chr4:87928626..87928670
-
Hg19::chr8:102064237..102064245,+p1@FLJ42969


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 monocyte1.33e-11842
CD14-positive, CD16-negative classical monocyte1.33e-11842
defensive cell4.83e-10348
phagocyte4.83e-10348
myeloid lineage restricted progenitor cell9.28e-9466
granulocyte monocyte progenitor cell2.73e-9267
myeloid leukocyte9.47e-9172
monopoietic cell3.00e-8159
monocyte3.00e-8159
monoblast3.00e-8159
promonocyte3.00e-8159
macrophage dendritic cell progenitor1.95e-7861
myeloid cell1.01e-58108
common myeloid progenitor1.01e-58108
stuff accumulating cell3.56e-5487
hematopoietic lineage restricted progenitor cell3.87e-49120
leukocyte3.18e-48136
nongranular leukocyte6.84e-42115
hematopoietic stem cell6.90e-38168
angioblastic mesenchymal cell6.90e-38168
hematopoietic oligopotent progenitor cell1.95e-37161
hematopoietic multipotent progenitor cell1.95e-37161
hematopoietic cell1.20e-35177
histamine secreting cell2.54e-185
biogenic amine secreting cell2.54e-185
granulocytopoietic cell2.54e-185
mast cell2.54e-185
mast cell progenitor2.54e-185
basophil mast progenitor cell2.54e-185
mesenchymal cell1.33e-14354
connective tissue cell3.44e-14361
motile cell9.76e-13386
multi fate stem cell5.87e-11427
somatic stem cell1.03e-10433
stem cell2.15e-10441
endocrine cell3.13e-109
Uber Anatomy
Ontology termp-valuen
bone marrow8.79e-8176
bone element1.70e-7482
skeletal element2.11e-6790
hematopoietic system3.38e-6598
blood island3.38e-6598
immune system4.73e-6593
skeletal system4.13e-60100
hemolymphoid system1.22e-58108
musculoskeletal system1.29e-33167
lateral plate mesoderm2.31e-28203
mesoderm5.54e-16315
mesoderm-derived structure5.54e-16315
presumptive mesoderm5.54e-16315
connective tissue1.26e-13371


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)
MA0003.10.138892
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.114225
MA0017.11.9612
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.000309691
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.11.53836
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.11.16085
MA0103.10.587485
MA0105.10.645738
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.12.0906
MA0115.11.02805
MA0116.10.935607
MA0117.11.93331
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.515404
MA0146.13.16699
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.20.00623756
MA0138.20.534556
MA0002.20.725804
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.22.02459
MA0065.22.13353
MA0150.11.4246
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.989789
MA0155.10.245306
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.948902
MA0160.10.386031
MA0161.10
MA0162.10.0809571
MA0163.10.387319
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.22.78803
MA0079.20.0134506
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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
CCNT2#90563.456109951070530.003468924173267830.0176220133144569
FOS#235354.089979685861090.004390678752314330.0208094980129314
FOSL1#8061414.44130171504470.0001149634866085920.0015725830488428
HMGN3#932464.46102603091850.0008897032402091330.00662812730609898
HSF1#3297344.80654545454553.57812328587162e-050.0006929271608625
JUN#372555.687649632880150.0009977588181358180.00715300200489338
JUNB#3726513.91392393628231.45501238171169e-050.000346308199939808
JUND#372763.815271241020560.002059794693458660.0119545928307935
MAFF#23764315.35873358816690.0008295092695633240.00631206692924765
MAFK#797549.854812050119970.0004960613405399460.00438606081481979
NFE2#4778321.05570745044430.000331303457282740.0033750489441233
SIRT6#51548227.93425527091360.00223909203745440.012860833377314



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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