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FF:12182-129A4: 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 16:48, 29 March 2012


Name:Whole blood (ribopure), donor090612, 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
sexNA
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)NA
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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0787
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.132
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-Whole0.217
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-Whole0.361
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: CNhs11672

Jaspar motifP-value
MA0002.28.41912e-12
MA0003.10.0358
MA0004.10.643
MA0006.10.507
MA0007.10.892
MA0009.10.0807
MA0014.10.956
MA0017.10.0548
MA0018.20.245
MA0019.10.775
MA0024.10.00927
MA0025.10.225
MA0027.10.589
MA0028.10.643
MA0029.10.737
MA0030.10.0271
MA0031.13.58069e-4
MA0035.26.34146e-4
MA0038.10.0512
MA0039.20.126
MA0040.10.115
MA0041.10.156
MA0042.10.0693
MA0043.10.0998
MA0046.10.586
MA0047.20.193
MA0048.10.103
MA0050.17.46691e-6
MA0051.10.0232
MA0052.10.0843
MA0055.10.0372
MA0057.10.964
MA0058.10.628
MA0059.10.592
MA0060.19.2617e-4
MA0061.10.0159
MA0062.21.63826e-4
MA0065.20.149
MA0066.10.246
MA0067.10.89
MA0068.10.606
MA0069.10.796
MA0070.10.0269
MA0071.10.55
MA0072.10.724
MA0073.10.266
MA0074.10.69
MA0076.10.198
MA0077.10.22
MA0078.10.914
MA0079.20.933
MA0080.21.18686e-17
MA0081.10.00158
MA0083.10.672
MA0084.10.551
MA0087.10.764
MA0088.10.426
MA0090.10.0261
MA0091.10.416
MA0092.10.863
MA0093.10.502
MA0099.20.326
MA0100.10.975
MA0101.10.336
MA0102.22.38069e-6
MA0103.10.156
MA0104.20.565
MA0105.11.79821e-4
MA0106.10.591
MA0107.10.358
MA0108.22.56597e-4
MA0111.10.302
MA0112.20.00104
MA0113.10.895
MA0114.10.393
MA0115.10.606
MA0116.12.45923e-5
MA0117.10.852
MA0119.10.479
MA0122.10.255
MA0124.10.862
MA0125.10.0429
MA0131.10.511
MA0135.10.324
MA0136.11.14988e-23
MA0137.20.0329
MA0138.20.376
MA0139.10.211
MA0140.17.46312e-11
MA0141.10.607
MA0142.10.776
MA0143.10.785
MA0144.10.0457
MA0145.10.0986
MA0146.10.00627
MA0147.10.497
MA0148.10.525
MA0149.10.536
MA0150.10.00212
MA0152.10.142
MA0153.10.134
MA0154.10.0022
MA0155.10.601
MA0156.15.0319e-18
MA0157.10.00309
MA0159.10.171
MA0160.10.362
MA0162.10.346
MA0163.11.26111e-4
MA0164.10.357
MA0258.10.0203
MA0259.10.299



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: CNhs11672

Novel motifP-value
10.189
100.0913
1000.562
1010.359
1020.613
1030.121
1040.818
1050.103
1060.0483
1070.772
1080.785
1090.0853
110.102
1100.345
1110.291
1120.111
1130.174
1140.0596
1150.258
1161
1170.0648
1180.359
1190.452
120.382
1200.664
1210.648
1220.257
1230.23
1240.0629
1250.13
1260.187
1270.32
1280.0469
1290.513
130.844
1300.965
1310.578
1320.398
1330.859
1340.971
1350.329
1360.99
1370.0055
1380.0703
1390.015
140.186
1400.519
1410.401
1420.984
1430.00335
1440.937
1450.357
1460.858
1470.232
1480.274
1490.57
150.0553
1500.999
1510.263
1520.348
1530.709
1540.969
1550.21
1560.727
1570.348
1580.0888
1590.3
160.454
1600.618
1610.459
1620.574
1630.332
1640.282
1650.127
1660.9
1670.783
1680.0558
1690.0112
170.376
180.375
190.343
20.228
200.596
210.603
220.174
230.0511
240.0707
250.156
260.137
270.0956
280.479
290.477
30.0979
300.858
310.531
320.864
330.549
340.219
350.284
360.418
370.163
380.301
390.996
40.87
400.331
410.0284
420.266
430.144
440.447
450.365
460.132
470.207
480.294
490.138
50.236
500.981
510.405
520.411
530.153
540.252
550.131
560.254
570.721
580.0565
590.0522
60.619
600.0464
610.273
620.0147
630.518
640.393
650.181
660.577
670.208
680.405
690.717
70.14
700.0642
710.114
720.208
730.351
740.822
750.131
760.649
770.644
780.369
790.978
80.501
800.00932
810.37
820.0198
830.518
840.498
850.161
860.119
870.592
880.516
890.217
90.249
900.0296
910.339
920.0719
930.206
940.0828
950.605
960.109
970.776
980.0444
990.447



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: CNhs11672


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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