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FF:11408-118E4: 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 17:07, 29 March 2012


Name:Adipocyte - subcutaneous, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueadipose tissue
dev stage42 years old adult
sexfemale
age42
cell typeadipocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1382
catalog numberCA803sD-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.422
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-0.452
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: CNhs12017

Jaspar motifP-value
MA0002.20.462
MA0003.10.102
MA0004.10.664
MA0006.10.378
MA0007.10.0296
MA0009.10.0516
MA0014.10.566
MA0017.10.168
MA0018.21.02574e-4
MA0019.10.0544
MA0024.16.91606e-5
MA0025.10.238
MA0027.10.556
MA0028.10.113
MA0029.10.873
MA0030.10.276
MA0031.10.598
MA0035.20.749
MA0038.10.89
MA0039.20.291
MA0040.10.796
MA0041.10.33
MA0042.10.927
MA0043.10.0101
MA0046.10.99
MA0047.20.444
MA0048.10.301
MA0050.12.76561e-4
MA0051.10.0324
MA0052.10.307
MA0055.10.967
MA0057.10.119
MA0058.10.477
MA0059.10.511
MA0060.10.489
MA0061.10.00138
MA0062.28.8496e-7
MA0065.22.85559e-4
MA0066.10.249
MA0067.10.0387
MA0068.10.821
MA0069.10.148
MA0070.10.727
MA0071.10.00622
MA0072.10.234
MA0073.10.9
MA0074.10.476
MA0076.10.0427
MA0077.10.582
MA0078.10.229
MA0079.20.541
MA0080.24.86181e-10
MA0081.10.0208
MA0083.10.362
MA0084.10.495
MA0087.10.848
MA0088.10.493
MA0090.10.31
MA0091.10.0453
MA0092.10.072
MA0093.10.744
MA0099.22.64034e-9
MA0100.10.131
MA0101.14.75555e-5
MA0102.20.0967
MA0103.10.00422
MA0104.20.843
MA0105.10.028
MA0106.10.317
MA0107.18.66161e-5
MA0108.20.141
MA0111.10.567
MA0112.20.0252
MA0113.10.0272
MA0114.12.68671e-4
MA0115.10.35
MA0116.10.7
MA0117.10.0191
MA0119.10.134
MA0122.10.97
MA0124.10.482
MA0125.10.184
MA0131.10.469
MA0135.10.252
MA0136.13.73571e-12
MA0137.20.0199
MA0138.20.0361
MA0139.10.457
MA0140.10.433
MA0141.10.00998
MA0142.10.504
MA0143.10.663
MA0144.10.185
MA0145.10.0939
MA0146.10.0171
MA0147.10.873
MA0148.10.759
MA0149.10.847
MA0150.10.0102
MA0152.10.712
MA0153.10.261
MA0154.10.952
MA0155.10.0441
MA0156.18.51777e-14
MA0157.10.809
MA0159.10.709
MA0160.10.068
MA0162.10.129
MA0163.10.427
MA0164.11
MA0258.10.311
MA0259.10.473



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: CNhs12017

Novel motifP-value
10.899
100.893
1000.374
1010.345
1020.165
1030.406
1040.596
1050.112
1060.938
1070.744
1080.258
1090.882
110.443
1100.703
1110.863
1120.29
1130.0234
1140.572
1150.151
1160.335
1170.37
1180.721
1190.786
120.793
1200.738
1210.731
1220.909
1230.143
1240.388
1250.0358
1260.932
1270.992
1280.507
1290.332
130.862
1300.681
1310.664
1320.234
1330.284
1340.578
1350.612
1360.279
1370.171
1380.273
1390.755
140.405
1400.847
1410.434
1420.58
1430.461
1440.0605
1450.729
1460.423
1470.942
1480.767
1490.0991
150.652
1500.337
1510.99
1520.326
1530.724
1540.145
1550.3
1560.57
1570.375
1580.0065
1590.208
160.132
1600.105
1610.906
1620.307
1630.725
1640.209
1650.578
1660.788
1670.786
1680.539
1690.0157
170.668
180.821
194.78837e-4
20.286
200.953
210.0685
220.0391
230.632
240.627
250.435
260.255
270.351
280.0329
290.58
30.695
300.393
310.169
320.0343
330.591
340.469
350.849
360.117
370.257
380.592
390.167
40.78
400.586
410.39
420.289
430.455
440.679
450.589
460.925
470.854
480.602
490.985
50.856
500.48
510.626
520.574
530.296
540.792
550.688
560.565
570.665
580.554
590.32
60.52
600.853
610.486
620.555
630.208
640.917
650.289
660.137
670.967
680.0487
690.335
70.681
700.918
710.83
720.958
730.0529
740.919
750.519
760.676
770.0239
780.487
790.711
80.122
800.317
810.915
820.142
830.508
840.476
850.152
860.768
870.0543
880.516
890.171
90.314
900.128
910.413
920.524
930.413
940.566
950.901
960.656
970.708
980.347
990.0456



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: CNhs12017


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)
0002521 (subcutaneous fat cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001013 (adipose tissue)
0001062 (anatomical entity)
0002190 (subcutaneous adipose tissue)
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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