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FF:12176-128I7: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:38, 29 March 2012


Name:Whole blood (ribopure), donor090325, donation1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationMatched_genome_OSC(contact:Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ribopure_minelute_cleanup-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0.0928
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0622
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0928
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.169
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.586
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11075

Jaspar motifP-value
MA0002.21.01537e-10
MA0003.10.0873
MA0004.10.656
MA0006.10.759
MA0007.10.9
MA0009.10.043
MA0014.10.847
MA0017.10.0795
MA0018.20.0261
MA0019.10.23
MA0024.10.0253
MA0025.10.451
MA0027.10.346
MA0028.10.296
MA0029.10.864
MA0030.10.212
MA0031.10.0028
MA0035.20.00162
MA0038.10.011
MA0039.20.253
MA0040.10.797
MA0041.10.634
MA0042.10.787
MA0043.10.566
MA0046.10.231
MA0047.20.406
MA0048.10.175
MA0050.13.03356e-7
MA0051.10.00892
MA0052.10.00324
MA0055.10.0612
MA0057.10.767
MA0058.10.719
MA0059.10.698
MA0060.12.41143e-4
MA0061.10.0423
MA0062.23.16202e-6
MA0065.20.109
MA0066.10.387
MA0067.10.557
MA0068.10.248
MA0069.10.712
MA0070.10.0189
MA0071.10.651
MA0072.10.584
MA0073.10.486
MA0074.10.915
MA0076.10.0563
MA0077.10.126
MA0078.10.91
MA0079.20.811
MA0080.21.09049e-17
MA0081.10.00149
MA0083.10.197
MA0084.10.537
MA0087.10.968
MA0088.10.125
MA0090.10.00635
MA0091.10.393
MA0092.10.922
MA0093.10.529
MA0099.20.0873
MA0100.10.996
MA0101.10.96
MA0102.20.00235
MA0103.10.109
MA0104.20.879
MA0105.11.03512e-4
MA0106.10.481
MA0107.10.848
MA0108.21.37801e-7
MA0111.10.146
MA0112.20.00356
MA0113.10.845
MA0114.10.406
MA0115.10.874
MA0116.12.64377e-6
MA0117.10.646
MA0119.10.575
MA0122.10.285
MA0124.10.664
MA0125.10.185
MA0131.10.8
MA0135.10.697
MA0136.11.27385e-24
MA0137.20.371
MA0138.20.682
MA0139.10.117
MA0140.19.40385e-10
MA0141.10.82
MA0142.10.971
MA0143.10.868
MA0144.10.245
MA0145.10.295
MA0146.10.00447
MA0147.10.761
MA0148.10.929
MA0149.10.332
MA0150.10.099
MA0152.10.116
MA0153.10.0675
MA0154.10.00374
MA0155.10.905
MA0156.11.41001e-18
MA0157.10.00547
MA0159.10.193
MA0160.10.673
MA0162.10.548
MA0163.15.45462e-7
MA0164.10.545
MA0258.10.027
MA0259.10.364



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11075

Novel motifP-value
10.162
100.0355
1000.72
1010.203
1020.84
1030.263
1040.64
1050.21
1060.0809
1070.737
1080.81
1090.138
110.105
1100.386
1110.26
1120.185
1130.142
1140.0952
1150.276
1160.806
1170.016
1180.472
1190.392
120.63
1200.576
1210.817
1220.421
1230.00626
1240.115
1250.172
1260.329
1270.409
1280.0724
1290.561
130.802
1300.544
1310.783
1320.589
1330.686
1340.93
1350.436
1360.919
1370.0105
1380.0883
1390.0326
140.15
1400.939
1410.41
1420.652
1430.00311
1440.65
1450.195
1460.705
1470.0672
1480.164
1490.436
150.0807
1500.97
1510.21
1520.621
1530.595
1540.78
1550.178
1560.695
1570.14
1580.271
1590.152
160.545
1600.617
1610.242
1620.69
1630.378
1640.235
1650.0704
1660.845
1670.809
1680.104
1690.0271
170.512
180.615
190.468
20.304
200.698
210.34
220.348
230.22
240.103
250.224
260.238
270.0801
280.453
290.374
30.0573
300.667
310.614
320.411
330.726
340.297
350.168
360.251
370.178
380.405
390.986
40.765
400.444
410.193
420.17
430.193
440.362
450.636
460.139
470.16
480.257
490.113
50.23
500.994
510.489
520.637
530.0502
540.357
550.0568
560.261
570.504
580.0579
590.121
60.769
600.12
610.223
620.0225
630.528
640.38
650.253
660.533
670.395
680.448
690.512
70.196
700.0612
710.093
720.195
730.413
740.609
750.0774
760.252
770.705
780.302
790.934
80.454
800.0225
810.263
820.0186
830.846
840.215
850.341
860.125
870.673
880.56
890.619
90.3
900.0154
910.334
920.0962
930.366
940.114
950.36
960.133
970.656
980.083
990.369



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11075


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000061 (anatomical structure)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002390 (hematopoietic system)
0004535 (cardiovascular system)
0007023 (adult organism)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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