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FF:12858-137D5: 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_rep3 (A3 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-penis0.048
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-lymphoma0.631
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: CNhs12952

Jaspar motifP-value
MA0002.20.88
MA0003.10.227
MA0004.10.53
MA0006.10.383
MA0007.10.453
MA0009.10.813
MA0014.10.725
MA0017.10.00253
MA0018.20.0101
MA0019.10.718
MA0024.11.50387e-7
MA0025.10.685
MA0027.10.497
MA0028.10.229
MA0029.10.763
MA0030.10.829
MA0031.10.692
MA0035.20.148
MA0038.15.39959e-4
MA0039.20.925
MA0040.10.146
MA0041.10.196
MA0042.10.484
MA0043.10.377
MA0046.10.74
MA0047.20.29
MA0048.10.216
MA0050.10.0466
MA0051.10.423
MA0052.12.65962e-4
MA0055.10.124
MA0057.10.409
MA0058.10.415
MA0059.10.925
MA0060.16.05018e-13
MA0061.10.0188
MA0062.20.284
MA0065.20.00322
MA0066.10.25
MA0067.10.356
MA0068.10.421
MA0069.10.697
MA0070.10.0276
MA0071.10.48
MA0072.10.318
MA0073.10.398
MA0074.10.204
MA0076.10.128
MA0077.10.27
MA0078.10.835
MA0079.20.817
MA0080.22.87398e-9
MA0081.10.0634
MA0083.10.179
MA0084.10.197
MA0087.10.377
MA0088.10.354
MA0090.10.639
MA0091.10.0515
MA0092.10.195
MA0093.10.391
MA0099.22.80924e-4
MA0100.10.239
MA0101.10.0402
MA0102.20.0356
MA0103.10.0239
MA0104.20.352
MA0105.10.00653
MA0106.10.187
MA0107.10.0102
MA0108.20.0632
MA0111.10.841
MA0112.20.00107
MA0113.10.621
MA0114.10.0996
MA0115.10.202
MA0116.10.0176
MA0117.10.461
MA0119.10.145
MA0122.10.632
MA0124.10.624
MA0125.10.0181
MA0131.10.252
MA0135.10.0903
MA0136.11.22422e-7
MA0137.20.144
MA0138.20.0303
MA0139.10.25
MA0140.10.319
MA0141.10.139
MA0142.10.118
MA0143.10.965
MA0144.10.0545
MA0145.10.0971
MA0146.10.0955
MA0147.10.409
MA0148.10.0891
MA0149.10.553
MA0150.10.252
MA0152.10.11
MA0153.10.296
MA0154.10.023
MA0155.10.2
MA0156.10.0212
MA0157.10.15
MA0159.10.0135
MA0160.10.2
MA0162.10.147
MA0163.15.20067e-4
MA0164.10.979
MA0258.10.0481
MA0259.10.29



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: CNhs12952

Novel motifP-value
10.398
100.888
1000.403
1010.858
1020.539
1030.0209
1040.699
1050.666
1061.99431e-4
1070.0311
1080.607
1090.171
110.112
1100.407
1110.353
1120.023
1130.462
1140.027
1150.135
1160.814
1170.674
1180.427
1190.0757
120.728
1200.21
1210.388
1220.621
1230.975
1240.413
1250.117
1260.254
1270.644
1280.00678
1290.198
130.607
1300.0516
1310.268
1320.311
1330.692
1340.922
1350.108
1360.556
1370.23
1380.663
1390.00354
140.463
1400.235
1410.452
1420.871
1430.0189
1440.514
1450.128
1460.754
1470.838
1480.0655
1490.0935
150.519
1500.545
1510.207
1520.0203
1530.181
1540.614
1550.601
1560.518
1570.463
1580.759
1590.572
160.195
1600.339
1610.941
1620.835
1630.865
1640.664
1650.683
1660.696
1670.0908
1680.151
1690.0335
170.12
180.0704
190.141
20.232
200.287
210.793
220.189
230.0131
240.77
250.935
260.527
270.0227
280.903
290.547
30.104
300.426
310.491
320.0689
330.627
340.334
350.238
360.689
370.136
380.32
390.105
40.432
400.489
410.144
420.326
430.158
440.0168
450.13
460.137
470.355
480.527
490.253
50.388
500.411
510.517
520.148
530.843
540.301
550.078
560.456
570.839
580.185
590.0785
60.492
600.0322
610.987
620.0876
630.161
640.495
650.0233
660.145
670.653
680.602
690.686
70.774
700.00708
710.29
720.0684
730.0511
740.299
750.544
760.698
770.107
780.666
790.00291
80.311
800.197
810.431
820.0257
830.775
840.842
850.00148
860.364
870.699
880.376
890.00809
90.174
900.363
910.402
920.127
930.828
940.0333
950.343
960.414
970.973
980.237
990.524



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: CNhs12952


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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