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FF:12760-136B6: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100385
|fonse_cell_line=FF:0100385
|fonse_cell_line_closure=FF:0100385
|fonse_cell_line_closure=FF:0100385

Revision as of 17:27, 29 March 2012


Name:Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep2 (A2 T0)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
ageNA
cell typeosteoblast
cell lineSaos-2
companyNA
collaborationKim Summers (Roslin Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.147
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-lymphoma0.586
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs12859

Jaspar motifP-value
MA0002.20.318
MA0003.10.205
MA0004.10.651
MA0006.10.478
MA0007.10.555
MA0009.10.465
MA0014.10.488
MA0017.10.0027
MA0018.20.0175
MA0019.10.67
MA0024.12.98201e-6
MA0025.10.893
MA0027.10.431
MA0028.10.511
MA0029.10.928
MA0030.10.58
MA0031.10.291
MA0035.20.165
MA0038.10.00588
MA0039.20.562
MA0040.10.112
MA0041.10.0299
MA0042.10.212
MA0043.10.971
MA0046.10.658
MA0047.20.0992
MA0048.10.152
MA0050.10.011
MA0051.10.169
MA0052.10.0015
MA0055.10.145
MA0057.10.48
MA0058.10.606
MA0059.10.957
MA0060.14.2783e-12
MA0061.10.0152
MA0062.20.92
MA0065.20.00402
MA0066.10.178
MA0067.10.393
MA0068.10.976
MA0069.10.726
MA0070.10.00941
MA0071.10.543
MA0072.10.752
MA0073.10.622
MA0074.10.523
MA0076.10.49
MA0077.10.12
MA0078.10.954
MA0079.20.55
MA0080.22.61347e-11
MA0081.10.0219
MA0083.10.275
MA0084.10.561
MA0087.10.38
MA0088.10.63
MA0090.10.763
MA0091.10.133
MA0092.10.13
MA0093.10.516
MA0099.21.69684e-6
MA0100.10.351
MA0101.10.0289
MA0102.20.00211
MA0103.10.0359
MA0104.20.459
MA0105.10.00324
MA0106.10.106
MA0107.10.00511
MA0108.20.189
MA0111.10.989
MA0112.20.00101
MA0113.10.677
MA0114.10.0759
MA0115.10.597
MA0116.10.012
MA0117.10.478
MA0119.10.0926
MA0122.10.347
MA0124.10.647
MA0125.10.0282
MA0131.10.393
MA0135.10.275
MA0136.18.40873e-12
MA0137.20.0483
MA0138.20.0759
MA0139.10.2
MA0140.10.125
MA0141.10.38
MA0142.10.21
MA0143.10.869
MA0144.10.0515
MA0145.10.064
MA0146.10.137
MA0147.10.52
MA0148.10.0375
MA0149.10.988
MA0150.10.0872
MA0152.10.392
MA0153.10.15
MA0154.10.0209
MA0155.10.35
MA0156.19.8592e-4
MA0157.10.0537
MA0159.10.0141
MA0160.10.205
MA0162.10.135
MA0163.14.57296e-4
MA0164.10.973
MA0258.10.0256
MA0259.10.329



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: CNhs12859

Novel motifP-value
10.325
100.897
1000.529
1010.55
1020.521
1030.0305
1040.647
1050.219
1066.49749e-4
1070.0406
1080.957
1090.14
110.114
1100.325
1110.274
1120.072
1130.249
1140.0272
1150.81
1160.916
1170.674
1180.43
1190.0549
120.933
1200.974
1210.605
1220.523
1230.152
1240.177
1250.0938
1260.274
1270.744
1280.00775
1290.248
130.419
1300.0548
1310.243
1320.22
1330.301
1340.793
1350.119
1360.392
1370.183
1380.869
1390.00134
140.308
1400.554
1410.648
1420.843
1430.0132
1440.656
1450.067
1460.266
1470.907
1480.111
1490.097
150.318
1500.727
1510.152
1520.0354
1530.147
1540.692
1550.441
1560.594
1570.418
1580.454
1590.623
160.333
1600.439
1610.716
1620.872
1630.856
1640.684
1650.221
1660.536
1670.186
1680.163
1690.0306
170.214
180.192
190.162
20.286
200.291
210.993
220.199
230.0185
240.965
250.81
260.662
270.0442
280.963
290.668
30.0784
300.467
310.621
320.412
330.424
340.357
350.257
360.208
370.125
380.284
390.208
40.71
400.313
410.201
420.181
430.139
440.255
450.121
460.231
470.268
480.449
490.158
50.256
500.368
510.619
520.215
530.43
540.373
550.0632
560.419
570.908
580.13
590.304
60.661
600.0404
610.989
620.0758
630.142
640.491
650.0316
660.233
670.901
680.706
690.975
70.538
700.00903
710.251
720.0683
730.0748
740.213
750.539
760.462
770.137
780.564
790.0752
80.39
800.0582
810.428
820.0405
830.356
840.56
850.00242
860.417
870.907
880.274
890.0282
90.228
900.295
910.484
920.0831
930.525
940.0407
950.38
960.216
970.647
980.292
990.485



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: CNhs12859


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)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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