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FF:11327-117E4: 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 17:03, 29 March 2012


Name:Adipocyte - breast, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebreast
dev stage40 years old adult
sexfemale
age40
cell typeadipocyte
cell lineNA
companyZenbio
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
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-penis0.285
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-0.203
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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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: CNhs11969

Jaspar motifP-value
MA0002.20.319
MA0003.10.205
MA0004.10.564
MA0006.10.0823
MA0007.10.303
MA0009.10.427
MA0014.10.618
MA0017.10.638
MA0018.26.38206e-6
MA0019.10.22
MA0024.10.00113
MA0025.10.00463
MA0027.10.687
MA0028.10.00443
MA0029.10.498
MA0030.10.0587
MA0031.10.117
MA0035.20.0127
MA0038.10.0722
MA0039.20.0428
MA0040.10.642
MA0041.10.611
MA0042.10.993
MA0043.13.25716e-5
MA0046.10.132
MA0047.20.588
MA0048.10.314
MA0050.11.09709e-4
MA0051.10.00783
MA0052.10.237
MA0055.10.911
MA0057.10.187
MA0058.10.481
MA0059.10.781
MA0060.15.46434e-5
MA0061.10.00137
MA0062.22.29566e-10
MA0065.20.0519
MA0066.10.376
MA0067.10.0215
MA0068.10.518
MA0069.10.0169
MA0070.10.903
MA0071.10.252
MA0072.10.842
MA0073.10.861
MA0074.10.477
MA0076.19.82301e-5
MA0077.10.612
MA0078.10.533
MA0079.20.49
MA0080.21.07145e-7
MA0081.10.0187
MA0083.10.0584
MA0084.10.96
MA0087.10.809
MA0088.10.696
MA0090.10.00204
MA0091.10.312
MA0092.10.132
MA0093.10.467
MA0099.26.90014e-9
MA0100.10.793
MA0101.17.08948e-6
MA0102.20.0536
MA0103.10.00565
MA0104.20.0373
MA0105.10.0392
MA0106.10.496
MA0107.11.09344e-6
MA0108.20.365
MA0111.10.689
MA0112.22.33419e-4
MA0113.10.17
MA0114.10.156
MA0115.10.492
MA0116.10.455
MA0117.10.189
MA0119.10.0949
MA0122.10.534
MA0124.10.19
MA0125.10.292
MA0131.10.211
MA0135.10.306
MA0136.14.79584e-12
MA0137.20.927
MA0138.20.0023
MA0139.10.83
MA0140.10.0481
MA0141.10.198
MA0142.10.247
MA0143.10.439
MA0144.10.438
MA0145.10.135
MA0146.10.414
MA0147.10.0727
MA0148.10.743
MA0149.10.829
MA0150.10.00379
MA0152.10.0705
MA0153.10.715
MA0154.10.433
MA0155.10.174
MA0156.19.80243e-12
MA0157.10.489
MA0159.10.268
MA0160.10.989
MA0162.10.0609
MA0163.10.246
MA0164.10.917
MA0258.10.139
MA0259.10.191



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: CNhs11969

Novel motifP-value
10.785
100.533
1000.993
1010.378
1020.275
1030.38
1040.953
1050.00657
1060.0447
1070.0789
1080.148
1090.771
110.9
1100.738
1110.306
1120.345
1130.332
1140.409
1158.59646e-4
1160.121
1170.512
1180.429
1190.737
120.575
1200.645
1210.578
1220.087
1230.0226
1240.933
1250.746
1260.988
1270.627
1280.166
1290.915
130.795
1300.694
1310.979
1320.366
1330.789
1340.571
1350.72
1360.128
1370.834
1380.395
1390.706
140.186
1400.275
1410.57
1420.798
1430.547
1440.829
1450.773
1460.694
1470.157
1480.757
1490.00524
150.703
1500.432
1510.581
1520.0286
1530.64
1540.478
1550.114
1560.314
1570.923
1580.0121
1590.559
160.0194
1600.362
1610.98
1620.414
1630.257
1640.197
1650.607
1660.155
1670.475
1680.914
1690.013
170.592
180.441
190.00148
20.225
200.435
210.156
220.134
230.411
240.272
250.403
260.354
270.352
280.118
290.861
30.906
300.471
310.48
324.99107e-11
330.556
340.852
350.844
360.0456
370.107
380.414
390.208
40.524
400.236
410.676
420.122
430.364
440.165
450.756
460.618
470.926
480.952
490.728
50.985
500.656
510.81
520.394
530.0597
540.88
550.485
560.583
570.974
580.524
590.105
60.244
600.511
610.468
620.898
630.396
640.695
650.623
660.175
670.755
680.303
690.849
70.631
700.937
710.379
720.375
730.00876
740.314
750.441
760.491
770.00934
780.858
790.00884
80.375
800.121
810.589
820.389
830.555
840.177
850.00845
860.482
870.0545
880.961
890.131
90.63
900.894
910.996
920.254
930.844
940.665
950.418
960.902
970.67
980.877
990.0242



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: CNhs11969


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)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000136 (fat cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002617 (adipocyte of breast)

UBERON: Anatomy
0000061 (anatomical structure)
0000310 (breast)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000915 (thoracic segment of trunk)
0001062 (anatomical entity)
0001443 (chest)
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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