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FF:11276-116H7: 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 16:44, 29 March 2012


Name:Osteoblast - differentiated, donor1
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
sexfemale
ageembryo 22week
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 number1419
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-0.203
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-0.453
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: CNhs11311

Jaspar motifP-value
MA0002.20.601
MA0003.10.141
MA0004.10.984
MA0006.10.345
MA0007.10.995
MA0009.10.0288
MA0014.10.177
MA0017.10.482
MA0018.22.91406e-6
MA0019.10.589
MA0024.11.5154e-5
MA0025.10.162
MA0027.10.734
MA0028.10.00389
MA0029.10.553
MA0030.10.444
MA0031.10.801
MA0035.20.257
MA0038.10.106
MA0039.20.0613
MA0040.10.186
MA0041.10.291
MA0042.10.313
MA0043.10.0157
MA0046.10.0394
MA0047.20.535
MA0048.10.422
MA0050.12.00231e-6
MA0051.10.13
MA0052.10.634
MA0055.10.547
MA0057.10.369
MA0058.10.913
MA0059.10.923
MA0060.11.79571e-4
MA0061.10.264
MA0062.22.94757e-7
MA0065.20.197
MA0066.10.931
MA0067.10.0188
MA0068.10.446
MA0069.10.464
MA0070.10.625
MA0071.10.895
MA0072.10.504
MA0073.10.984
MA0074.10.347
MA0076.10.00651
MA0077.10.217
MA0078.10.939
MA0079.20.508
MA0080.23.47402e-7
MA0081.10.0598
MA0083.11.60005e-4
MA0084.10.51
MA0087.10.593
MA0088.10.403
MA0090.11.6446e-4
MA0091.10.0152
MA0092.10.148
MA0093.10.987
MA0099.20.865
MA0100.10.277
MA0101.10.0549
MA0102.20.14
MA0103.10.0151
MA0104.20.241
MA0105.10.0941
MA0106.10.181
MA0107.10.265
MA0108.28.55082e-4
MA0111.10.16
MA0112.20.542
MA0113.10.0278
MA0114.10.302
MA0115.10.0161
MA0116.10.133
MA0117.10.259
MA0119.10.745
MA0122.10.813
MA0124.10.74
MA0125.10.282
MA0131.10.287
MA0135.10.605
MA0136.13.81886e-8
MA0137.20.433
MA0138.20.71
MA0139.10.955
MA0140.10.669
MA0141.10.983
MA0142.10.459
MA0143.10.676
MA0144.10.487
MA0145.10.512
MA0146.10.593
MA0147.10.187
MA0148.10.409
MA0149.10.741
MA0150.10.0621
MA0152.10.198
MA0153.10.0105
MA0154.10.316
MA0155.10.125
MA0156.11.70807e-6
MA0157.10.874
MA0159.10.328
MA0160.10.379
MA0162.10.245
MA0163.10.859
MA0164.10.562
MA0258.10.91
MA0259.10.651



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: CNhs11311

Novel motifP-value
10.348
100.124
1000.384
1010.724
1020.145
1030.608
1040.548
1050.952
1060.756
1070.128
1080.925
1090.618
110.909
1100.99
1110.268
1120.459
1130.0372
1140.887
1150.731
1160.466
1170.101
1180.292
1190.275
120.442
1200.944
1210.824
1220.589
1231.17819e-4
1240.795
1250.823
1260.415
1270.73
1280.407
1290.9
130.072
1300.158
1310.113
1320.285
1330.47
1340.2
1350.34
1360.235
1370.111
1380.743
1390.503
140.417
1400.145
1410.014
1420.982
1430.525
1440.318
1450.659
1460.222
1470.356
1480.0902
1490.0927
150.452
1500.816
1510.762
1520.0329
1530.58
1540.747
1550.0158
1560.809
1570.768
1580.00287
1590.248
160.202
1600.264
1610.603
1620.236
1630.523
1640.681
1650.847
1660.0555
1670.312
1680.631
1690.14
170.665
180.239
190.024
20.236
200.107
210.61
220.304
230.532
240.915
250.216
260.666
270.714
280.083
290.837
30.985
300.0985
310.608
321.92039e-11
330.585
340.594
350.334
360.169
370.759
380.581
390.304
40.449
400.312
410.43
420.471
430.969
440.632
450.384
460.926
470.3
480.663
490.621
50.81
500.773
510.9
520.36
530.183
540.866
550.277
560.463
570.973
580.311
590.0667
60.313
600.562
610.687
620.345
630.723
640.633
650.839
660.648
670.566
680.229
690.529
70.253
700.354
710.385
720.647
730.0689
740.907
750.387
760.133
770.32
780.00342
790.0316
80.556
800.968
810.95
820.717
830.785
840.131
850.751
860.885
870.474
880.416
890.131
90.229
900.488
910.884
920.152
930.658
940.878
950.0819
960.434
970.425
980.941
990.00239



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: CNhs11311


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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