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Coexpression cluster:C512: Difference between revisions

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{{Coexpression_clusters
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539,0.335616,0.648411,0.265293,0.624798,0.183311,0.547862,0.125402,0.0085505,0.362671,0.83378,0.54332,0.0501047,0.763881,0.752371,0.600675,0.723852,0.00199364,0.0391361,0.450842,0.505205,0.680147,0.738704,0.594826,0.146875,0.808026,0.271939,0.569592,0.264579,0.0191624,0.678071,0.688781,0.457605,0.742029,0.65266,0.58825,0.185312,0.0155425,0.741891,0.147939,0.281488,0.282255,0.625848,0.385757,0.220774,0.282081,0.0306956,0.838076,0.172443,0.354484,0.0783337,5.21405e-05,0.398723,0.461844,0.328182,0.184057,0.326996,0.48466,0.337521,0.378673,0.56258,0.15359,0.0306472,0.340182,0.430665,0.201185,0.581027,0.746375,0.878019,0.601265,0.72428,0.233748,0.546704,0.830335,0.387159,0.458329,1.45259e-05,0.257156,0.00708055,0.323734,0.115636,0.571615,0.282931,0.749886,0.150592,0.0552811,0.0247318,0.0908675,0.522191,0.185105,0.781357,0.168024,0.0107067,0.363115,0.590036,0.322755,0.00856959,0.0954589,0.450043,0.445395,0.687533,0.0202807,0.0534531,0.453778,0.41671,0.898367,0.677018,0.645799,0.00343399,0.357633,0.124142,0.472167,0.779178,0.686837,0.641805,0.180642,0.0328,0.402522,0.504214|tfbs_overrepresentation_for_novel_motifs=0.132318,1.07164,0.401452,0.226461,0.336835,0.63973,0.283394,0.691671,1.05646,0.327423,0.203249,0.318077,0.120712,1.38039,0.334774,0.370545,1.1846,0.546349,2.26562,1.24323,0.12778,1.13137,0.219533,0.329158,0.156949,0.336616,0.462972,1.1683,0.104779,0.411748,0.550528,0.502277,0.465343,0.540435,0.285802,0.283823,0.5899,0.2261,0.905465,0.619603,0.283797,0.176475,1.25286,0.101392,0.130655,0.450639,0.776062,0.569177,1.49743,0.104852,0.348337,0.293583,1.44796,0.571408,0.712611,0.758765,0.707757,0.251346,0.411389,0.250577,0.538962,0.286121,0.0444464,0.445454,0.300385,0.415664,0.795966,1.15172,0.493047,0.993712,0.167519,0.0475211,0.14141,0.710737,0.0277888,0.103174,1.86549,1.10062,0.490165,0.152902,0.326109,0.444519,0.300103,0.0463558,0.662744,0.00390547,0.108261,0.652631,0.370044,1.24919,0.885103,0.637733,0.517273,0.482989,0.103441,0.515572,1.74754,0.555608,0.373917,0.872407,0.910526,0.512221,0.550563,1.19152,0.405789,0.200011,0.45903,0.27168,0.474718,0.0941477,0.419252,0.548062,0.392758,0.210038,0.839147,0.585863,0.126573,0.186928,0.413654,0.490021,0.702982,0.368007,0.22321,0.309149,0.945405,0.431436,0.278404,0.521744,0.742996,0.517952,0.638371,0.555366,0.756554,0.30647,0.897471,1.28827,1.03328,0.21836,0.856781,1.69932,1.30076,0.82115,0.765828,0.552418,0.407293,0.244914,0.393075,1.5412,0.174198,0.217844,0.257994,0.00309082,0.638724,0.654278,0.779441,2.33366,0.938093,0.315972,0.475228,0.845713,0.819992,0.621644,1.22694,0.433659,0.421111,0.299472,0.445457,0.282346,2.36685|tfbs_overrepresentation_jaspar=MA0003.1;0.528528,MA0004.1;1.12587,MA0006.1;0.101986,MA0007.1;2.39542,MA0009.1;0.600198,MA0014.1;0.122675,MA0017.1;0.789059,MA0019.1;0.322194,MA0024.1;0.50459,MA0025.1;0.725013,MA0027.1;2.18072,MA0028.1;0.111328,MA0029.1;0.522011,MA0030.1;0.511665,MA0031.1;0.454061,MA0038.1;0.285594,MA0040.1;1.3076,MA0041.1;0.220669,MA0042.1;0.197306,MA0043.1;0.60049,MA0046.1;0.590147,MA0048.1;0.151328,MA0050.1;0.197941,MA0051.1;0.77145,MA0052.1;1.31505,MA0055.1;0.129781,MA0056.1;0,MA0057.1;0.288482,MA0058.1;0.435867,MA0059.1;0.433767,MA0060.1;0.0444001,MA0061.1;0.321845,MA0063.1;0,MA0066.1;0.285934,MA0067.1;0.900956,MA0068.1;1.07794,MA0069.1;0.586593,MA0070.1;0.576293,MA0071.1;0.255111,MA0072.1;0.572162,MA0073.1;0.35411,MA0074.1;0.281628,MA0076.1;0.151641,MA0077.1;0.565087,MA0078.1;0.363755,MA0081.1;1.99114,MA0083.1;0.607144,MA0084.1;1.08294,MA0087.1;0.569916,MA0088.1;0.277816,MA0089.1;0,MA0090.1;0.161293,MA0091.1;0.601165,MA0092.1;1.02629,MA0093.1;1.14302,MA0095.1;0,MA0098.1;0,MA0100.1;0.296726,MA0101.1;0.343779,MA0103.1;0.0967439,MA0105.1;0.121083,MA0106.1;0.854542,MA0107.1;0.871747,MA0108.2;0.451357,MA0109.1;0,MA0111.1;0.170509,MA0113.1;0.884817,MA0114.1;0.852422,MA0115.1;0.827474,MA0116.1;0.516883,MA0117.1;0.635078,MA0119.1;0.407815,MA0122.1;0.659244,MA0124.1;0.787807,MA0125.1;0.708116,MA0130.1;0,MA0131.1;0.379172,MA0132.1;0,MA0133.1;0,MA0135.1;0.628343,MA0136.1;0.791942,MA0139.1;0.123548,MA0140.1;0.253051,MA0141.1;1.37252,MA0142.1;0.426146,MA0143.1;0.885144,MA0144.1;0.798544,MA0145.1;0.319303,MA0146.1;0.252061,MA0147.1;0.525775,MA0148.1;0.640121,MA0149.1;0.245595,MA0062.2;0.131354,MA0035.2;0.252505,MA0039.2;0.0782174,MA0138.2;1.70306,MA0002.2;1.90535,MA0137.2;0.743725,MA0104.2;0.168935,MA0047.2;0.832232,MA0112.2;0.98042,MA0065.2;3.59866,MA0150.1;0.476082,MA0151.1;0,MA0152.1;0.258148,MA0153.1;0.692238,MA0154.1;0.664419,MA0155.1;0.665536,MA0156.1;0.749879,MA0157.1;0.402372,MA0158.1;0,MA0159.1;0.527394,MA0160.1;0.236884,MA0161.1;0,MA0162.1;0.06468,MA0163.1;0.0140121,MA0164.1;0.907835,MA0080.2;2.28555,MA0018.2;0.320136,MA0099.2;2.03839,MA0079.2;0.0919123,MA0102.2;1.11935,MA0258.1;0.436156,MA0259.1;0.257452,MA0442.1;0}}
|full_id=C512_Mast_immature_Basophils_CD14_CD34_Peripheral_Natural
|id=C512
}}

Latest revision as of 11:24, 17 September 2013


Full id: C512_Mast_immature_Basophils_CD14_CD34_Peripheral_Natural



Phase1 CAGE Peaks

Hg19::chr11:62321050..62321060,-p@chr11:62321050..62321060
-
Hg19::chr11:62321151..62321162,+p2@AF083120
Hg19::chr11:62321179..62321195,+p1@AF083120
Hg19::chr14:105947776..105947788,-p@chr14:105947776..105947788
-
Hg19::chr14:90379258..90379271,+p@chr14:90379258..90379271
+
Hg19::chr15:86124719..86124731,-p@chr15:86124719..86124731
-
Hg19::chr17:76320888..76320910,+p@chr17:76320888..76320910
+
Hg19::chr19:6065937..6065958,-p@chr19:6065937..6065958
-
Hg19::chr19:6067480..6067495,+p@chr19:6067480..6067495
+
Hg19::chr1:156095033..156095048,-p@chr1:156095033..156095048
-
Hg19::chr1:156095991..156096021,-p@chr1:156095991..156096021
-
Hg19::chr1:156096337..156096353,+p6@LMNA
Hg19::chr22:29707363..29707374,+p@chr22:29707363..29707374
+
Hg19::chr2:157188649..157188663,+p@chr2:157188649..157188663
+
Hg19::chr2:235244225..235244257,-p@chr2:235244225..235244257
-
Hg19::chr2:235244770..235244800,+p@chr2:235244770..235244800
+
Hg19::chr8:26467187..26467198,+p@chr8:26467187..26467198
+
Hg19::chr8:26467208..26467221,+p@chr8:26467208..26467221
+


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 monocyte2.03e-9042
CD14-positive, CD16-negative classical monocyte2.03e-9042
defensive cell1.49e-7748
phagocyte1.49e-7748
granulocyte monocyte progenitor cell2.82e-7067
myeloid leukocyte7.16e-6872
macrophage dendritic cell progenitor4.41e-6761
myeloid lineage restricted progenitor cell1.39e-6466
monopoietic cell1.50e-6259
monocyte1.50e-6259
monoblast1.50e-6259
promonocyte1.50e-6259
leukocyte2.44e-55136
myeloid cell1.79e-51108
common myeloid progenitor1.79e-51108
hematopoietic lineage restricted progenitor cell1.97e-48120
hematopoietic stem cell9.42e-47168
angioblastic mesenchymal cell9.42e-47168
nongranular leukocyte3.70e-46115
hematopoietic cell1.59e-43177
hematopoietic oligopotent progenitor cell3.53e-42161
hematopoietic multipotent progenitor cell3.53e-42161
stuff accumulating cell1.84e-4187
mesenchymal cell4.00e-25354
connective tissue cell2.81e-24361
intermediate monocyte3.03e-229
CD14-positive, CD16-positive monocyte3.03e-229
motile cell2.70e-21386
stem cell4.04e-18441
multi fate stem cell1.19e-17427
somatic stem cell3.78e-17433
basophil4.91e-093
natural killer cell2.78e-083
pro-NK cell2.78e-083
single nucleate cell3.64e-083
mononuclear cell3.64e-083
non-classical monocyte3.91e-083
CD14-low, CD16-positive monocyte3.91e-083
somatic cell1.21e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow4.66e-6676
bone element3.00e-6082
hematopoietic system1.91e-5598
blood island1.91e-5598
skeletal element1.06e-5390
immune system1.56e-5193
hemolymphoid system5.36e-49108
skeletal system5.57e-47100
lateral plate mesoderm6.03e-27203
connective tissue4.02e-23371
musculoskeletal system9.84e-23167
mesoderm1.01e-12315
mesoderm-derived structure1.01e-12315
presumptive mesoderm1.01e-12315


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)
MA0003.10.528528
MA0004.11.12587
MA0006.10.101986
MA0007.12.39542
MA0009.10.600198
MA0014.10.122675
MA0017.10.789059
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.111328
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.11.3076
MA0041.10.220669
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.151328
MA0050.10.197941
MA0051.10.77145
MA0052.11.31505
MA0055.10.129781
MA0056.10
MA0057.10.288482
MA0058.10.435867
MA0059.10.433767
MA0060.10.0444001
MA0061.10.321845
MA0063.10
MA0066.10.285934
MA0067.10.900956
MA0068.11.07794
MA0069.10.586593
MA0070.10.576293
MA0071.10.255111
MA0072.10.572162
MA0073.10.35411
MA0074.10.281628
MA0076.10.151641
MA0077.10.565087
MA0078.10.363755
MA0081.11.99114
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.277816
MA0089.10
MA0090.10.161293
MA0091.10.601165
MA0092.11.02629
MA0093.11.14302
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.343779
MA0103.10.0967439
MA0105.10.121083
MA0106.10.854542
MA0107.10.871747
MA0108.20.451357
MA0109.10
MA0111.10.170509
MA0113.10.884817
MA0114.10.852422
MA0115.10.827474
MA0116.10.516883
MA0117.10.635078
MA0119.10.407815
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.791942
MA0139.10.123548
MA0140.10.253051
MA0141.11.37252
MA0142.10.426146
MA0143.10.885144
MA0144.10.798544
MA0145.10.319303
MA0146.10.252061
MA0147.10.525775
MA0148.10.640121
MA0149.10.245595
MA0062.20.131354
MA0035.20.252505
MA0039.20.0782174
MA0138.21.70306
MA0002.21.90535
MA0137.20.743725
MA0104.20.168935
MA0047.20.832232
MA0112.20.98042
MA0065.23.59866
MA0150.10.476082
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.10.664419
MA0155.10.665536
MA0156.10.749879
MA0157.10.402372
MA0158.10
MA0159.10.527394
MA0160.10.236884
MA0161.10
MA0162.10.06468
MA0163.10.0140121
MA0164.10.907835
MA0080.22.28555
MA0018.20.320136
MA0099.22.03839
MA0079.20.0919123
MA0102.21.11935
MA0258.10.436156
MA0259.10.257452
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
CEBPB#105193.985573812912410.0001279638982483860.0017013903970927
EP300#203383.010640767210310.002449702240952020.0137899235887882
ESR1#209946.837467399145440.002365870939017020.0134054467773437
FOS#235383.999091248397510.0003621391833294120.00361754702704356
FOSL1#8061613.23785990545773.63408313806019e-060.000119352204042726
FOSL2#235554.702833501267140.003213902471153850.0168527770339327
GATA2#2624117.788569392727441.30664820082503e-089.63736097782242e-07
JUN#3725106.951571773520192.54111005088979e-071.32101041615171e-05
JUNB#372658.502953516616980.0002227847834503680.0024821228929777
JUND#372772.72014708850540.009101573110983490.034441798403493
MAX#414972.509327142391660.01407392076042370.0493906656686121
MEF2A#420544.165162424365350.01356346165085610.0478808305341815
MEF2C#420849.18030099836090.0007993388687331780.0061733455676717
NR3C1#290875.822842406567299.74743006618345e-050.00138618171116848
POLR2A#5430141.670241359545170.00716503966421080.0297538599399806
SMARCA4#6597326.12765055131470.0001966726141823860.00236366986796251
SMARCC1#6599512.12871092211994.19750190632436e-050.000760289458193913
SMARCC2#6601315.69256240448290.0008663104654238830.00646446118165225
SMC3#912654.179148012481350.005339096119768960.024529731640531
SPI1#668873.190570253314390.003725697551062360.0185758402890821



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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