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FF:12184-129A6: 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 17:02, 29 March 2012


Name:Whole blood (ribopure), donor090612, donation3
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-penis0.196
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.254
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.37
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.222
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-Whole0.413
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: CNhs11949

Jaspar motifP-value
MA0002.22.46686e-8
MA0003.10.0824
MA0004.10.48
MA0006.10.428
MA0007.10.916
MA0009.10.0635
MA0014.10.852
MA0017.10.107
MA0018.20.0106
MA0019.10.208
MA0024.10.0125
MA0025.10.379
MA0027.10.452
MA0028.10.821
MA0029.10.666
MA0030.10.349
MA0031.10.00106
MA0035.29.68221e-5
MA0038.10.00141
MA0039.20.482
MA0040.10.35
MA0041.10.749
MA0042.10.639
MA0043.10.347
MA0046.10.239
MA0047.20.505
MA0048.10.246
MA0050.14.84187e-7
MA0051.10.0282
MA0052.10.00593
MA0055.10.0477
MA0057.10.906
MA0058.10.471
MA0059.10.51
MA0060.11.38249e-5
MA0061.10.108
MA0062.20.00848
MA0065.20.127
MA0066.10.29
MA0067.10.428
MA0068.10.876
MA0069.10.629
MA0070.10.00403
MA0071.10.617
MA0072.10.761
MA0073.10.185
MA0074.10.576
MA0076.10.724
MA0077.10.425
MA0078.10.829
MA0079.20.696
MA0080.23.81245e-17
MA0081.10.005
MA0083.10.505
MA0084.10.535
MA0087.10.998
MA0088.10.306
MA0090.10.0211
MA0091.10.223
MA0092.10.799
MA0093.10.346
MA0099.20.0426
MA0100.10.937
MA0101.10.949
MA0102.20.00742
MA0103.10.128
MA0104.20.334
MA0105.15.53908e-4
MA0106.10.385
MA0107.10.75
MA0108.21.14959e-5
MA0111.10.217
MA0112.20.00191
MA0113.10.746
MA0114.10.42
MA0115.10.748
MA0116.11.21947e-5
MA0117.10.562
MA0119.10.493
MA0122.10.394
MA0124.10.74
MA0125.10.142
MA0131.10.594
MA0135.10.497
MA0136.15.58318e-21
MA0137.20.963
MA0138.20.293
MA0139.10.194
MA0140.18.6472e-14
MA0141.10.717
MA0142.10.353
MA0143.10.304
MA0144.10.359
MA0145.10.121
MA0146.10.00125
MA0147.10.347
MA0148.10.967
MA0149.10.409
MA0150.10.146
MA0152.10.0654
MA0153.10.0148
MA0154.10.00536
MA0155.10.88
MA0156.11.17448e-12
MA0157.10.00248
MA0159.10.12
MA0160.10.721
MA0162.10.447
MA0163.11.5882e-5
MA0164.10.754
MA0258.10.0106
MA0259.10.209



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: CNhs11949

Novel motifP-value
10.164
100.0494
1000.757
1010.177
1020.545
1030.367
1040.835
1050.247
1060.0191
1070.438
1080.936
1090.134
110.0934
1100.342
1110.293
1120.101
1130.224
1140.0536
1150.795
1160.541
1170.0431
1180.407
1190.287
120.384
1200.534
1210.89
1220.545
1230.0122
1240.327
1250.17
1260.427
1270.289
1280.0556
1290.58
130.782
1300.436
1310.767
1320.969
1330.756
1340.724
1350.512
1360.728
1370.0115
1380.0397
1390.0169
140.235
1400.591
1410.5
1420.607
1430.00102
1440.686
1450.122
1460.916
1470.0673
1480.275
1490.535
150.0857
1500.811
1510.189
1520.216
1530.539
1540.576
1550.197
1560.585
1570.13
1580.435
1590.0905
160.376
1600.575
1610.3
1620.871
1630.243
1640.13
1650.151
1660.95
1670.91
1680.173
1690.0124
170.293
180.56
190.234
20.216
200.666
210.106
220.239
230.179
240.0385
250.272
260.143
270.154
280.496
290.362
30.0707
300.743
310.518
320.978
330.647
340.327
350.198
360.47
370.175
380.324
390.837
40.886
400.473
410.255
420.219
430.169
440.303
450.507
460.106
470.111
480.229
490.116
50.452
500.905
510.377
520.452
530.0781
540.264
550.138
560.253
570.538
580.0726
590.0538
60.644
600.0626
610.279
620.017
630.496
640.393
650.182
660.346
670.273
680.256
690.241
70.222
700.0492
710.115
720.301
730.205
740.768
750.0921
760.384
770.575
780.187
790.543
80.248
800.102
810.215
820.0189
830.411
840.128
850.146
860.0838
870.38
880.672
890.682
90.324
900.0245
910.41
920.0715
930.632
940.194
950.399
960.0519
970.643
980.0641
990.802



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: CNhs11949


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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