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FF:11357-117H7: 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 - visceral, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stage59 years old adult
sexmale
age59
cell typepreadipocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2115
catalog numberCA802s-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
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-lymphoma0.222
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: CNhs11982

Jaspar motifP-value
MA0002.20.731
MA0003.10.369
MA0004.10.15
MA0006.10.293
MA0007.10.611
MA0009.10.414
MA0014.10.756
MA0017.10.779
MA0018.22.99962e-7
MA0019.10.968
MA0024.10.0368
MA0025.10.0124
MA0027.10.365
MA0028.10.174
MA0029.10.856
MA0030.10.0122
MA0031.10.0256
MA0035.20.0196
MA0038.10.00717
MA0039.20.0833
MA0040.10.459
MA0041.10.903
MA0042.10.818
MA0043.13.76556e-7
MA0046.10.231
MA0047.20.963
MA0048.10.72
MA0050.10.631
MA0051.10.264
MA0052.10.0031
MA0055.10.0362
MA0057.10.234
MA0058.10.0574
MA0059.10.804
MA0060.14.80997e-10
MA0061.10.207
MA0062.26.36122e-4
MA0065.20.362
MA0066.10.0744
MA0067.10.00481
MA0068.10.162
MA0069.10.314
MA0070.10.564
MA0071.10.951
MA0072.10.276
MA0073.10.995
MA0074.10.179
MA0076.10.0284
MA0077.10.596
MA0078.10.932
MA0079.20.448
MA0080.21.59238e-4
MA0081.10.0259
MA0083.10.332
MA0084.10.0897
MA0087.10.468
MA0088.10.169
MA0090.10.12
MA0091.10.00747
MA0092.10.486
MA0093.10.15
MA0099.20.0029
MA0100.10.476
MA0101.10.452
MA0102.20.217
MA0103.10.153
MA0104.20.289
MA0105.10.00162
MA0106.10.0194
MA0107.10.585
MA0108.20.47
MA0111.10.476
MA0112.20.0011
MA0113.10.412
MA0114.10.867
MA0115.10.653
MA0116.10.00233
MA0117.10.238
MA0119.10.0499
MA0122.10.392
MA0124.10.436
MA0125.10.175
MA0131.10.237
MA0135.10.233
MA0136.12.1831e-4
MA0137.20.424
MA0138.20.701
MA0139.10.369
MA0140.10.188
MA0141.10.427
MA0142.10.103
MA0143.10.772
MA0144.10.411
MA0145.10.312
MA0146.10.357
MA0147.10.639
MA0148.10.588
MA0149.10.791
MA0150.10.425
MA0152.10.0525
MA0153.10.135
MA0154.10.0391
MA0155.10.502
MA0156.12.54676e-4
MA0157.10.0961
MA0159.10.522
MA0160.10.571
MA0162.10.135
MA0163.13.05529e-7
MA0164.10.811
MA0258.10.105
MA0259.10.457



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: CNhs11982

Novel motifP-value
10.236
100.0968
1000.889
1010.738
1020.788
1030.059
1040.958
1050.491
1060.0168
1070.0136
1080.314
1090.151
110.157
1100.127
1110.526
1120.0826
1130.355
1140.159
1150.0172
1160.0455
1170.239
1180.939
1190.703
120.239
1200.0229
1210.601
1220.0271
1230.303
1240.328
1250.177
1260.813
1270.307
1280.0978
1290.807
130.92
1300.909
1310.642
1320.862
1330.437
1340.723
1350.588
1360.824
1370.587
1380.537
1390.662
140.422
1400.31
1410.807
1420.372
1430.0242
1440.63
1450.57
1460.845
1470.269
1480.00515
1490.0146
150.547
1500.207
1510.539
1520.0728
1530.968
1540.884
1550.204
1560.479
1570.834
1580.0654
1590.472
160.0368
1600.198
1610.585
1620.53
1630.782
1640.422
1650.465
1660.193
1670.327
1680.522
1690.0124
170.39
180.081
190.0222
20.141
200.0801
210.0709
220.272
230.105
240.505
250.479
260.0637
270.109
280.412
290.0929
30.164
300.412
310.774
321.15539e-5
330.774
340.513
350.173
360.0804
370.105
380.713
390.148
40.848
400.256
410.876
420.562
430.16
440.113
450.802
460.0387
470.16
480.286
490.602
50.844
500.712
510.324
520.754
530.694
540.562
550.12
560.472
570.475
580.92
590.0128
60.716
600.405
610.589
620.31
630.332
640.488
650.165
660.506
670.261
680.306
690.777
70.808
700.405
710.0243
720.836
730.085
740.0071
750.307
760.895
770.0411
780.58
790.0122
80.0204
800.699
810.319
820.353
830.332
840.36
850.314
860.303
870.128
880.752
890.0257
90.12
900.261
910.0539
920.2
930.622
940.287
950.0908
960.197
970.534
980.774
990.00623



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: CNhs11982


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)
0002582 (visceral preadipocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
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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