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FF:11467-119B9: 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 16:37, 29 March 2012


Name:Preadipocyte - breast, donor1
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 stage52 years old adult
sexfemale
age52
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-penis-0.102
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-0.405
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11052

Jaspar motifP-value
MA0002.20.996
MA0003.10.298
MA0004.10.195
MA0006.10.13
MA0007.10.778
MA0009.10.19
MA0014.10.216
MA0017.10.569
MA0018.21.543e-5
MA0019.10.527
MA0024.12.97593e-9
MA0025.10.00629
MA0027.10.379
MA0028.10.0912
MA0029.10.0712
MA0030.10.495
MA0031.10.698
MA0035.20.15
MA0038.10.00281
MA0039.20.00844
MA0040.10.344
MA0041.10.661
MA0042.10.955
MA0043.14.48644e-4
MA0046.10.341
MA0047.20.859
MA0048.10.563
MA0050.14.82457e-5
MA0051.10.0567
MA0052.10.643
MA0055.10.406
MA0057.10.473
MA0058.10.124
MA0059.10.927
MA0060.13.78831e-14
MA0061.10.0131
MA0062.25.97635e-6
MA0065.20.624
MA0066.10.555
MA0067.10.018
MA0068.10.877
MA0069.10.0144
MA0070.10.828
MA0071.10.88
MA0072.10.614
MA0073.10.807
MA0074.10.95
MA0076.10.0124
MA0077.10.782
MA0078.10.717
MA0079.20.874
MA0080.25.85271e-6
MA0081.10.0129
MA0083.10.314
MA0084.10.141
MA0087.10.406
MA0088.10.706
MA0090.12.59361e-8
MA0091.10.0141
MA0092.10.0284
MA0093.10.181
MA0099.20.0345
MA0100.10.677
MA0101.16.33085e-5
MA0102.20.238
MA0103.15.53641e-4
MA0104.20.0114
MA0105.10.138
MA0106.10.0272
MA0107.11.87241e-4
MA0108.20.532
MA0111.10.63
MA0112.20.00292
MA0113.10.115
MA0114.10.961
MA0115.10.0165
MA0116.10.284
MA0117.10.369
MA0119.10.273
MA0122.10.635
MA0124.10.229
MA0125.10.326
MA0131.10.19
MA0135.10.145
MA0136.12.35121e-7
MA0137.20.415
MA0138.20.344
MA0139.10.705
MA0140.10.896
MA0141.10.867
MA0142.10.259
MA0143.10.275
MA0144.10.844
MA0145.10.129
MA0146.10.86
MA0147.10.0558
MA0148.10.702
MA0149.10.877
MA0150.10.0989
MA0152.16.09427e-4
MA0153.10.937
MA0154.10.602
MA0155.10.289
MA0156.16.17782e-6
MA0157.10.889
MA0159.10.141
MA0160.10.146
MA0162.10.0717
MA0163.10.0431
MA0164.10.274
MA0258.10.37
MA0259.10.294



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: CNhs11052

Novel motifP-value
10.819
100.512
1000.516
1010.536
1020.0718
1030.597
1040.579
1050.168
1060.149
1070.277
1080.259
1090.586
110.892
1100.967
1110.814
1120.28
1130.107
1140.0394
1150.151
1160.198
1170.603
1180.174
1190.952
120.474
1200.95
1210.651
1220.394
1230.0118
1240.741
1250.854
1260.486
1270.434
1280.559
1290.941
130.622
1300.915
1310.299
1320.467
1330.324
1340.349
1350.526
1360.739
1370.727
1380.395
1390.117
140.202
1400.853
1410.899
1420.645
1430.447
1440.673
1450.642
1460.93
1470.266
1480.841
1495.42627e-5
150.683
1500.53
1510.519
1520.017
1530.0322
1540.944
1550.00213
1560.487
1570.568
1580.0217
1590.414
160.0228
1600.742
1610.501
1620.686
1630.288
1640.564
1650.911
1660.213
1670.579
1680.393
1690.0351
170.5
180.0683
190.0162
20.382
200.321
210.472
220.21
230.0904
240.109
250.474
260.777
270.521
280.233
290.969
30.514
300.528
310.632
323.11035e-14
330.967
340.778
350.771
360.0477
370.111
380.474
390.161
40.874
400.278
410.78
420.629
430.202
440.818
450.774
460.558
470.921
480.943
490.68
50.348
500.905
510.488
520.576
530.106
540.763
550.0361
560.898
570.959
580.308
590.299
60.535
600.678
610.308
620.862
630.587
640.716
650.518
660.329
670.557
680.769
690.582
70.366
700.322
710.183
720.706
730.0125
740.0568
750.679
760.467
770.113
780.349
790.0182
80.459
800.689
810.322
820.143
830.936
840.129
850.0839
860.481
870.213
880.909
890.0941
90.596
900.805
910.814
920.0253
930.713
940.646
950.371
960.238
970.295
980.387
990.0283



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: CNhs11052


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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