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FF:12179-129A1: 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), donor090309, 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-0.0338
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.11
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-Whole0.178
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-Whole0.481
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: CNhs11675

Jaspar motifP-value
MA0002.22.31591e-11
MA0003.10.04
MA0004.10.522
MA0006.10.502
MA0007.10.944
MA0009.10.0468
MA0014.10.971
MA0017.10.0688
MA0018.20.136
MA0019.10.958
MA0024.10.0188
MA0025.10.944
MA0027.10.515
MA0028.10.542
MA0029.10.443
MA0030.10.0131
MA0031.12.29207e-4
MA0035.22.61498e-5
MA0038.10.0383
MA0039.20.0992
MA0040.10.0542
MA0041.10.0516
MA0042.10.0266
MA0043.10.668
MA0046.10.371
MA0047.20.183
MA0048.10.0733
MA0050.11.11706e-6
MA0051.10.0106
MA0052.10.105
MA0055.10.038
MA0057.10.96
MA0058.10.563
MA0059.10.563
MA0060.19.95719e-4
MA0061.10.0298
MA0062.23.82314e-5
MA0065.20.149
MA0066.10.327
MA0067.10.929
MA0068.10.721
MA0069.10.885
MA0070.10.017
MA0071.10.73
MA0072.10.539
MA0073.10.324
MA0074.10.652
MA0076.10.144
MA0077.10.134
MA0078.10.972
MA0079.20.622
MA0080.21.67584e-17
MA0081.10.0012
MA0083.10.95
MA0084.10.736
MA0087.10.962
MA0088.10.289
MA0090.10.0138
MA0091.10.221
MA0092.10.866
MA0093.10.425
MA0099.20.891
MA0100.10.819
MA0101.10.521
MA0102.22.25757e-4
MA0103.10.18
MA0104.20.468
MA0105.15.41809e-4
MA0106.10.539
MA0107.10.659
MA0108.23.18031e-4
MA0111.10.314
MA0112.20.00182
MA0113.10.925
MA0114.10.494
MA0115.10.289
MA0116.12.70311e-5
MA0117.10.836
MA0119.10.575
MA0122.10.439
MA0124.10.844
MA0125.10.0379
MA0131.10.52
MA0135.10.175
MA0136.15.308e-24
MA0137.20.059
MA0138.20.475
MA0139.10.175
MA0140.15.62346e-16
MA0141.10.806
MA0142.10.955
MA0143.10.66
MA0144.10.0413
MA0145.10.0846
MA0146.10.00729
MA0147.10.429
MA0148.10.625
MA0149.10.486
MA0150.10.00899
MA0152.10.0593
MA0153.10.108
MA0154.10.0031
MA0155.10.602
MA0156.18.6641e-19
MA0157.10.00228
MA0159.10.134
MA0160.10.629
MA0162.10.515
MA0163.19.18308e-5
MA0164.10.462
MA0258.10.0385
MA0259.10.272



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: CNhs11675

Novel motifP-value
10.177
100.102
1000.513
1010.276
1020.551
1030.0927
1040.709
1050.206
1060.0465
1070.728
1080.81
1090.112
110.0905
1100.365
1110.533
1120.0825
1130.201
1140.0583
1150.31
1160.959
1170.0444
1180.319
1190.474
120.364
1200.586
1210.703
1220.238
1230.267
1240.0311
1250.14
1260.217
1270.218
1280.0346
1290.593
130.864
1300.607
1310.854
1320.536
1330.317
1340.871
1350.366
1360.893
1370.00644
1380.0777
1390.0302
140.165
1400.356
1410.502
1420.983
1430.00192
1440.599
1450.353
1460.731
1470.146
1480.206
1490.449
150.028
1500.836
1510.271
1520.256
1530.516
1540.89
1550.217
1560.708
1570.234
1580.251
1590.258
160.444
1600.762
1610.382
1620.664
1630.516
1640.257
1650.147
1660.798
1670.53
1680.0739
1690.0175
170.405
180.433
190.301
20.205
200.535
210.492
220.148
230.0625
240.017
250.194
260.238
270.0805
280.469
290.41
30.0893
300.835
310.455
320.75
330.611
340.199
350.291
360.52
370.148
380.304
390.939
40.881
400.405
410.0452
420.29
430.152
440.358
450.346
460.135
470.174
480.249
490.161
50.192
500.941
510.397
520.453
530.168
540.321
550.0727
560.253
570.91
580.064
590.0433
60.766
600.0466
610.267
620.0129
630.546
640.369
650.154
660.562
670.247
680.54
690.461
70.172
700.0346
710.111
720.209
730.261
740.562
750.0999
760.552
770.568
780.367
790.956
80.431
800.0096
810.332
820.0313
830.482
840.548
850.162
860.114
870.527
880.543
890.188
90.159
900.0443
910.514
920.0644
930.203
940.115
950.477
960.104
970.765
980.0629
990.494



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: CNhs11675


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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