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FF:11328-117E5: 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:Preadipocyte - 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 typepreadipocyte
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-penis0.0534
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-0.303
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: CNhs11971

Jaspar motifP-value
MA0002.20.566
MA0003.10.252
MA0004.10.545
MA0006.10.0975
MA0007.10.584
MA0009.10.309
MA0014.10.216
MA0017.10.74
MA0018.23.64976e-5
MA0019.10.549
MA0024.11.94203e-4
MA0025.10.00283
MA0027.10.545
MA0028.10.0156
MA0029.10.303
MA0030.10.118
MA0031.10.0789
MA0035.20.0482
MA0038.10.00655
MA0039.20.00733
MA0040.10.2
MA0041.10.742
MA0042.10.996
MA0043.14.98064e-5
MA0046.10.272
MA0047.20.417
MA0048.10.202
MA0050.13.02813e-5
MA0051.10.00267
MA0052.10.0655
MA0055.10.985
MA0057.10.237
MA0058.10.292
MA0059.10.582
MA0060.15.71477e-10
MA0061.10.0886
MA0062.29.99918e-7
MA0065.20.864
MA0066.10.259
MA0067.10.0174
MA0068.10.675
MA0069.10.0356
MA0070.10.775
MA0071.10.351
MA0072.10.483
MA0073.10.847
MA0074.10.176
MA0076.10.00171
MA0077.10.955
MA0078.10.865
MA0079.20.791
MA0080.25.07658e-7
MA0081.10.0139
MA0083.10.189
MA0084.10.518
MA0087.10.558
MA0088.10.601
MA0090.18.56278e-4
MA0091.10.0497
MA0092.10.193
MA0093.10.452
MA0099.24.57806e-5
MA0100.10.548
MA0101.14.45388e-4
MA0102.20.0361
MA0103.10.138
MA0104.20.0478
MA0105.10.372
MA0106.10.0763
MA0107.13.16606e-4
MA0108.20.662
MA0111.10.71
MA0112.21.17522e-4
MA0113.10.363
MA0114.10.757
MA0115.10.0662
MA0116.10.128
MA0117.10.2
MA0119.10.124
MA0122.10.406
MA0124.10.0166
MA0125.10.232
MA0131.10.237
MA0135.10.284
MA0136.11.59505e-10
MA0137.20.122
MA0138.20.0395
MA0139.10.952
MA0140.10.218
MA0141.10.461
MA0142.10.405
MA0143.10.306
MA0144.10.999
MA0145.10.213
MA0146.10.762
MA0147.10.117
MA0148.10.353
MA0149.10.68
MA0150.10.0236
MA0152.10.0318
MA0153.10.926
MA0154.10.323
MA0155.10.113
MA0156.12.43783e-8
MA0157.10.261
MA0159.10.0652
MA0160.10.351
MA0162.10.0751
MA0163.10.0145
MA0164.10.62
MA0258.10.0358
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: CNhs11971

Novel motifP-value
10.406
100.342
1000.996
1010.194
1020.269
1030.396
1040.677
1050.0598
1060.0472
1070.0396
1080.157
1090.478
110.384
1100.455
1110.359
1120.303
1130.243
1140.0303
1150.00852
1160.0461
1170.941
1180.452
1190.93
120.322
1200.31
1210.69
1220.181
1230.0506
1240.44
1250.815
1260.765
1270.52
1280.106
1290.941
130.956
1300.532
1310.973
1320.475
1330.864
1340.631
1350.529
1360.566
1370.537
1380.92
1390.222
140.28
1400.717
1410.991
1420.995
1430.431
1440.653
1450.904
1460.756
1470.176
1480.99
1490.00165
150.886
1500.421
1510.831
1520.00682
1530.193
1540.872
1550.105
1560.961
1570.574
1580.0281
1590.524
160.00914
1600.533
1610.7
1620.369
1630.614
1640.174
1650.752
1660.305
1670.54
1680.946
1690.0192
170.228
180.135
190.00428
20.302
200.602
210.283
220.223
230.237
240.131
250.43
260.266
270.441
280.264
290.658
30.4
300.679
310.475
321.12087e-16
330.727
340.88
350.624
360.0419
370.0784
380.749
390.293
40.96
400.59
410.944
420.386
430.191
440.0899
450.911
460.298
470.553
480.481
490.704
50.643
500.748
510.878
520.609
530.132
540.684
550.108
560.745
570.709
580.419
590.0338
60.514
600.504
610.785
620.803
630.279
640.776
650.388
660.244
670.551
680.334
690.414
70.411
700.296
710.271
720.731
730.00545
740.278
750.603
760.6
770.0323
780.834
790.00101
80.238
800.204
810.47
820.166
830.431
840.263
850.0319
860.468
870.116
880.816
890.0766
90.861
900.625
910.945
920.0745
930.39
940.907
950.187
960.942
970.659
980.941
990.0167



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: CNhs11971


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)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002334 (preadipocyte)
0002371 (somatic cell)
0002580 (preadipocyte of the 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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