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FF:11425-118G3: 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 17:08, 29 March 2012


Name:Osteoblast - differentiated, donor3
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 stage18 weeks old fetus
sexmale
ageembryo 18 week
cell typeosteocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1266
catalog numberCA406D-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-penis-0.072
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-lymphoma-0.294
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: CNhs12035

Jaspar motifP-value
MA0002.20.225
MA0003.10.127
MA0004.10.188
MA0006.10.158
MA0007.10.0889
MA0009.10.127
MA0014.10.872
MA0017.10.499
MA0018.20.00752
MA0019.10.3
MA0024.10.00119
MA0025.10.0926
MA0027.10.952
MA0028.10.00245
MA0029.10.469
MA0030.10.949
MA0031.10.416
MA0035.20.924
MA0038.10.352
MA0039.20.436
MA0040.10.893
MA0041.10.308
MA0042.10.603
MA0043.10.0273
MA0046.10.846
MA0047.20.792
MA0048.10.646
MA0050.11.98312e-4
MA0051.10.0136
MA0052.10.657
MA0055.10.793
MA0057.10.442
MA0058.10.0925
MA0059.10.892
MA0060.10.8
MA0061.10.136
MA0062.21.12364e-9
MA0065.20.623
MA0066.10.738
MA0067.10.0626
MA0068.10.937
MA0069.10.682
MA0070.10.363
MA0071.10.612
MA0072.10.79
MA0073.10.829
MA0074.10.32
MA0076.11.09542e-4
MA0077.10.794
MA0078.10.69
MA0079.20.328
MA0080.23.61176e-8
MA0081.12.52732e-4
MA0083.10.0667
MA0084.10.956
MA0087.10.846
MA0088.10.884
MA0090.10.0356
MA0091.10.0153
MA0092.10.263
MA0093.10.171
MA0099.20.083
MA0100.10.0269
MA0101.10.0129
MA0102.20.237
MA0103.10.397
MA0104.20.635
MA0105.10.0668
MA0106.10.936
MA0107.10.0155
MA0108.21.29209e-13
MA0111.10.217
MA0112.20.153
MA0113.10.0208
MA0114.10.259
MA0115.10.0345
MA0116.10.0868
MA0117.10.154
MA0119.10.182
MA0122.10.996
MA0124.10.143
MA0125.10.949
MA0131.10.131
MA0135.10.056
MA0136.12.53926e-11
MA0137.20.404
MA0138.20.104
MA0139.10.724
MA0140.10.557
MA0141.10.687
MA0142.10.536
MA0143.10.509
MA0144.10.93
MA0145.10.813
MA0146.10.285
MA0147.10.323
MA0148.10.418
MA0149.10.236
MA0150.10.0411
MA0152.10.703
MA0153.10.214
MA0154.10.803
MA0155.10.0419
MA0156.15.36284e-11
MA0157.10.416
MA0159.10.941
MA0160.10.461
MA0162.10.0403
MA0163.10.893
MA0164.10.571
MA0258.10.593
MA0259.10.317



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: CNhs12035

Novel motifP-value
10.407
100.151
1000.728
1010.588
1020.542
1030.634
1040.342
1050.866
1060.323
1070.0448
1080.286
1090.569
110.768
1100.807
1110.571
1120.892
1130.638
1140.366
1150.00379
1160.0313
1170.232
1180.457
1190.854
120.515
1200.115
1210.465
1220.228
1238.39511e-4
1240.0183
1250.916
1260.777
1270.971
1280.0469
1290.828
130.493
1300.343
1310.319
1320.0622
1330.182
1340.978
1350.915
1360.962
1370.019
1380.678
1390.798
140.82
1400.573
1410.117
1420.0581
1430.59
1440.877
1450.656
1460.139
1470.414
1480.862
1490.0396
150.352
1500.284
1510.517
1520.0098
1530.879
1540.144
1550.32
1560.748
1570.5
1580.1
1590.636
160.379
1600.495
1610.611
1620.27
1630.155
1640.703
1650.774
1660.103
1670.353
1680.955
1690.264
170.952
180.337
190.113
20.122
200.531
210.76
220.265
230.844
240.807
250.115
260.98
270.388
280.0614
290.341
30.448
300.375
310.243
323.19379e-8
330.684
340.648
350.342
360.128
370.211
380.946
390.496
40.937
400.777
410.113
420.0764
430.802
440.945
450.501
460.91
470.516
480.996
490.768
50.381
500.873
510.477
520.335
530.19
540.523
550.625
560.826
570.539
580.0973
590.0747
60.977
600.677
610.813
620.0933
630.779
640.787
650.201
660.727
670.94
680.267
690.334
70.128
700.977
710.243
720.863
730.00356
740.76
750.473
760.299
770.0936
780.179
790.0522
80.171
800.602
810.91
820.885
830.374
840.359
850.214
860.657
870.0733
880.33
890.112
90.269
900.00392
910.738
920.515
930.944
940.213
950.779
960.94
970.41
980.964
990.0179



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: CNhs12035


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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