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FF:11354-117H4: 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:Osteoblast, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone
dev stage22 weeks old fetus
sexmale
ageembryo 22week
cell typeosteoblast
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1428
catalog numberCA406-R10f
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.415
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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
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: CNhs11385

Jaspar motifP-value
MA0002.20.254
MA0003.10.269
MA0004.10.155
MA0006.10.394
MA0007.10.609
MA0009.10.993
MA0014.10.0866
MA0017.10.597
MA0018.26.57572e-5
MA0019.10.659
MA0024.10.0493
MA0025.10.0044
MA0027.10.501
MA0028.10.0363
MA0029.10.506
MA0030.10.0123
MA0031.10.0149
MA0035.20.121
MA0038.10.758
MA0039.20.00312
MA0040.10.729
MA0041.10.608
MA0042.10.482
MA0043.13.68888e-4
MA0046.10.797
MA0047.20.0543
MA0048.10.00251
MA0050.13.37959e-7
MA0051.12.65952e-6
MA0052.10.261
MA0055.10.964
MA0057.10.794
MA0058.10.076
MA0059.10.181
MA0060.10.811
MA0061.10.459
MA0062.23.42887e-7
MA0065.20.174
MA0066.10.414
MA0067.10.00522
MA0068.10.0198
MA0069.10.0931
MA0070.10.636
MA0071.10.804
MA0072.10.983
MA0073.10.845
MA0074.10.845
MA0076.10.00293
MA0077.10.908
MA0078.10.603
MA0079.20.231
MA0080.24.17549e-9
MA0081.10.00189
MA0083.14.00787e-5
MA0084.10.32
MA0087.10.556
MA0088.10.46
MA0090.10.00345
MA0091.10.255
MA0092.10.436
MA0093.10.175
MA0099.20.265
MA0100.10.0427
MA0101.10.00283
MA0102.20.00645
MA0103.10.00337
MA0104.20.886
MA0105.10.0348
MA0106.10.506
MA0107.10.00169
MA0108.20.54
MA0111.10.922
MA0112.20.128
MA0113.10.299
MA0114.10.153
MA0115.10.553
MA0116.10.0631
MA0117.10.943
MA0119.10.335
MA0122.10.0913
MA0124.10.874
MA0125.10.639
MA0131.10.814
MA0135.10.375
MA0136.11.99854e-6
MA0137.20.173
MA0138.20.844
MA0139.10.961
MA0140.10.868
MA0141.10.17
MA0142.10.62
MA0143.10.576
MA0144.10.288
MA0145.10.943
MA0146.10.246
MA0147.10.433
MA0148.10.383
MA0149.10.872
MA0150.10.181
MA0152.10.0168
MA0153.10.753
MA0154.10.246
MA0155.10.741
MA0156.16.52911e-6
MA0157.10.199
MA0159.10.619
MA0160.10.0714
MA0162.10.764
MA0163.10.143
MA0164.10.488
MA0258.10.636
MA0259.10.137



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: CNhs11385

Novel motifP-value
10.456
100.528
1000.55
1010.778
1020.245
1030.156
1040.89
1050.397
1060.399
1070.106
1080.981
1090.9
110.0723
1100.515
1110.557
1120.592
1130.0346
1140.359
1150.376
1160.272
1170.416
1180.272
1190.685
120.408
1200.514
1210.823
1220.141
1230.0057
1240.907
1250.239
1260.286
1270.792
1280.741
1290.964
130.404
1300.342
1310.315
1320.868
1330.234
1340.0322
1350.954
1360.0927
1370.583
1380.137
1390.562
140.3
1400.92
1410.545
1420.709
1430.126
1440.715
1450.928
1460.477
1470.0749
1480.266
1490.276
150.85
1500.566
1510.368
1520.447
1530.85
1540.52
1557.50796e-4
1560.715
1570.0142
1580.0267
1590.14
160.0596
1600.322
1610.111
1620.0465
1630.521
1640.485
1650.474
1660.0106
1670.899
1680.702
1690.627
170.816
180.161
190.044
20.56
200.122
210.254
220.655
230.122
240.678
250.738
260.875
270.853
280.217
290.714
30.337
300.518
310.8
323.48657e-6
330.934
340.773
350.601
360.303
370.49
380.509
390.273
40.235
400.0538
410.878
420.528
430.945
440.299
450.363
460.137
470.228
480.303
490.757
50.51
500.936
510.79
520.563
530.224
540.446
550.406
560.87
570.334
580.873
590.229
60.549
600.701
610.728
620.312
630.513
640.887
650.808
660.14
670.983
680.424
690.498
70.64
700.232
710.294
720.432
730.618
740.158
750.72
760.536
770.241
780.434
790.107
80.257
800.808
810.398
820.809
830.17
840.338
850.532
860.994
870.998
880.763
890.0464
90.529
900.044
910.314
920.487
930.168
940.425
950.161
960.583
970.696
980.287
990.0434



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: CNhs11385


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000035 (single fate stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000062 (osteoblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000335 (mesenchyme condensation cell)
0000375 (osteoprogenitor cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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