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FF:11353-117H3: 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 17:04, 29 March 2012


Name:Osteoblast - differentiated, 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 typeosteocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1424
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-0.207
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-0.569
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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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: CNhs11980

Jaspar motifP-value
MA0002.20.0116
MA0003.10.0987
MA0004.10.593
MA0006.10.261
MA0007.10.29
MA0009.10.574
MA0014.10.65
MA0017.10.182
MA0018.24.20683e-4
MA0019.10.834
MA0024.16.91195e-4
MA0025.10.0708
MA0027.10.349
MA0028.10.0359
MA0029.10.2
MA0030.10.682
MA0031.10.387
MA0035.20.91
MA0038.10.0159
MA0039.20.119
MA0040.10.627
MA0041.10.325
MA0042.10.549
MA0043.11.01807e-4
MA0046.10.212
MA0047.20.853
MA0048.10.938
MA0050.11.75586e-5
MA0051.10.0138
MA0052.10.962
MA0055.10.921
MA0057.10.196
MA0058.10.455
MA0059.10.229
MA0060.12.46798e-5
MA0061.10.594
MA0062.29.3307e-6
MA0065.20.0169
MA0066.10.0592
MA0067.10.0761
MA0068.10.166
MA0069.10.377
MA0070.10.503
MA0071.10.166
MA0072.10.967
MA0073.10.797
MA0074.10.186
MA0076.10.00204
MA0077.10.695
MA0078.10.365
MA0079.20.81
MA0080.24.17264e-6
MA0081.10.036
MA0083.10.0675
MA0084.10.973
MA0087.10.775
MA0088.10.737
MA0090.10.0861
MA0091.10.0262
MA0092.10.134
MA0093.10.683
MA0099.20.517
MA0100.10.3
MA0101.10.204
MA0102.20.042
MA0103.10.114
MA0104.20.931
MA0105.10.235
MA0106.10.0406
MA0107.10.332
MA0108.20.904
MA0111.10.924
MA0112.28.94411e-5
MA0113.10.138
MA0114.10.173
MA0115.10.0473
MA0116.10.126
MA0117.10.617
MA0119.10.146
MA0122.10.506
MA0124.10.0238
MA0125.10.601
MA0131.10.109
MA0135.10.706
MA0136.14.21875e-9
MA0137.20.498
MA0138.20.0962
MA0139.10.164
MA0140.10.586
MA0141.10.0275
MA0142.10.787
MA0143.10.772
MA0144.10.54
MA0145.10.217
MA0146.10.112
MA0147.10.94
MA0148.10.487
MA0149.10.273
MA0150.10.292
MA0152.10.788
MA0153.10.0535
MA0154.10.138
MA0155.10.0432
MA0156.17.59268e-6
MA0157.10.924
MA0159.10.252
MA0160.10.364
MA0162.10.0718
MA0163.10.00102
MA0164.10.165
MA0258.10.00349
MA0259.10.342



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: CNhs11980

Novel motifP-value
10.666
100.871
1000.917
1010.908
1020.722
1030.226
1040.138
1050.576
1060.0298
1070.0368
1080.229
1090.0851
110.0375
1100.287
1110.595
1120.402
1130.267
1140.207
1150.0161
1160.105
1170.729
1180.821
1190.194
120.632
1200.217
1210.543
1220.479
1230.363
1240.91
1250.945
1260.81
1270.21
1280.0348
1290.683
130.791
1300.576
1310.856
1320.396
1330.963
1340.169
1350.175
1360.761
1370.418
1380.957
1390.0997
140.845
1400.158
1410.527
1420.0536
1430.0754
1440.78
1450.186
1460.239
1470.46
1480.442
1490.00917
150.204
1500.345
1510.296
1520.0679
1530.87
1540.59
1550.425
1560.728
1570.171
1580.189
1590.654
160.0703
1600.133
1610.568
1620.0443
1630.0877
1640.448
1650.611
1660.121
1670.606
1680.718
1690.0367
170.178
180.0392
190.06
20.289
200.509
210.764
220.0891
230.187
240.792
250.573
260.299
270.205
280.613
290.415
30.341
300.425
310.367
321.75673e-7
330.757
340.535
350.333
360.858
370.145
380.409
390.257
40.703
400.286
410.926
420.781
430.16
440.213
450.256
460.13
470.323
480.188
490.17
50.61
500.519
510.266
520.323
530.771
540.326
550.0662
560.372
570.393
580.966
590.013
60.956
600.392
610.603
620.759
630.0748
640.153
650.0684
660.709
670.363
680.329
690.0811
70.853
700.0301
710.43
720.559
730.0438
740.729
750.377
760.753
770.0131
780.52
790.00129
80.0488
800.926
810.213
820.123
830.551
840.224
850.0785
860.444
870.226
880.601
890.0229
90.438
900.354
910.357
920.104
930.54
940.527
950.452
960.494
970.248
980.0631
990.021



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: CNhs11980


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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