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FF:11426-118G4: 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, 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 stage22 weeks old fetus
sexfemale
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 number1419
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-penis-0.0294
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-lymphoma0.137
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12036

Jaspar motifP-value
MA0002.20.128
MA0003.10.636
MA0004.10.566
MA0006.10.295
MA0007.10.875
MA0009.10.149
MA0014.10.434
MA0017.10.0864
MA0018.20.523
MA0019.10.253
MA0024.10.297
MA0025.10.512
MA0027.10.623
MA0028.10.26
MA0029.10.126
MA0030.10.248
MA0031.10.0353
MA0035.20.545
MA0038.10.237
MA0039.20.483
MA0040.10.806
MA0041.10.356
MA0042.10.623
MA0043.10.0558
MA0046.10.133
MA0047.20.609
MA0048.10.0472
MA0050.18.40424e-10
MA0051.16.77172e-4
MA0052.10.158
MA0055.10.356
MA0057.10.509
MA0058.10.377
MA0059.10.505
MA0060.10.00986
MA0061.10.00733
MA0062.20.00886
MA0065.20.029
MA0066.10.637
MA0067.10.155
MA0068.10.767
MA0069.10.619
MA0070.10.0689
MA0071.10.632
MA0072.10.6
MA0073.10.965
MA0074.10.915
MA0076.10.484
MA0077.10.596
MA0078.10.76
MA0079.20.222
MA0080.22.15651e-9
MA0081.10.011
MA0083.18.08546e-10
MA0084.10.364
MA0087.10.951
MA0088.10.186
MA0090.10.00221
MA0091.10.556
MA0092.10.664
MA0093.10.687
MA0099.20.0571
MA0100.10.789
MA0101.10.0878
MA0102.20.00311
MA0103.10.00665
MA0104.20.0413
MA0105.19.81256e-6
MA0106.10.812
MA0107.10.0327
MA0108.24.22823e-9
MA0111.10.0498
MA0112.20.0619
MA0113.10.922
MA0114.10.00855
MA0115.10.0993
MA0116.13.07242e-4
MA0117.10.945
MA0119.10.419
MA0122.10.9
MA0124.10.813
MA0125.10.725
MA0131.10.979
MA0135.10.0239
MA0136.12.28501e-9
MA0137.20.135
MA0138.20.768
MA0139.10.133
MA0140.10.8
MA0141.10.309
MA0142.10.636
MA0143.10.67
MA0144.10.22
MA0145.10.648
MA0146.10.911
MA0147.10.135
MA0148.10.514
MA0149.10.685
MA0150.10.233
MA0152.10.0756
MA0153.10.178
MA0154.10.00262
MA0155.10.518
MA0156.11.41332e-4
MA0157.10.173
MA0159.10.0216
MA0160.10.262
MA0162.10.948
MA0163.10.00243
MA0164.10.576
MA0258.10.0258
MA0259.10.672



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: CNhs12036

Novel motifP-value
10.0723
100.0326
1000.199
1010.0838
1020.399
1030.18
1040.545
1050.51
1060.379
1070.576
1080.963
1090.493
110.621
1100.431
1110.229
1120.0779
1130.0788
1140.392
1150.0828
1160.578
1170.0879
1180.183
1190.183
120.903
1200.591
1210.563
1220.91
1231.35057e-4
1240.059
1250.392
1260.387
1270.629
1280.552
1290.415
130.202
1300.136
1310.946
1320.583
1330.654
1340.188
1350.972
1360.645
1370.2
1380.131
1390.146
140.193
1400.0806
1410.0151
1420.252
1430.592
1440.618
1450.422
1460.951
1470.3
1480.00208
1490.81
150.232
1500.757
1510.484
1520.00598
1530.317
1540.48
1550.0343
1560.701
1570.167
1580.0108
1590.529
160.649
1600.977
1610.892
1620.517
1630.791
1640.258
1650.61
1660.199
1670.352
1680.778
1690.919
170.999
180.925
190.641
20.669
200.595
210.757
220.682
230.421
240.589
250.331
260.992
270.851
280.0943
290.702
30.161
300.219
310.891
321.08465e-6
330.838
340.936
350.0662
360.0142
370.749
380.212
390.754
40.462
400.285
410.288
420.244
430.259
440.731
450.979
460.421
470.155
480.321
490.115
50.295
500.935
510.585
520.774
530.0363
540.676
550.726
560.758
570.437
580.0946
590.548
60.535
600.272
610.348
620.136
630.603
640.499
650.723
660.332
670.614
680.0356
690.411
70.227
700.155
710.105
720.237
730.055
740.876
750.183
760.19
770.909
780.0585
790.299
80.953
800.631
810.288
820.277
830.429
840.476
850.565
860.459
870.172
880.447
890.82
90.628
900.028
910.37
920.547
930.766
940.243
950.978
960.178
970.577
980.155
990.00588



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: CNhs12036


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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