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FF:11336-117F4: 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 16:47, 29 March 2012


Name:Adipocyte - subcutaneous, donor2
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 stage41 years old adult
sexfemale
age41
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 number1375
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-penis-0.0407
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-0.388
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: CNhs11371

Jaspar motifP-value
MA0002.20.304
MA0003.10.0571
MA0004.10.51
MA0006.10.719
MA0007.10.0968
MA0009.10.294
MA0014.10.685
MA0017.10.0888
MA0018.21.20544e-6
MA0019.10.325
MA0024.14.08995e-4
MA0025.18.27138e-4
MA0027.10.456
MA0028.10.105
MA0029.10.571
MA0030.10.178
MA0031.10.929
MA0035.20.93
MA0038.10.013
MA0039.20.173
MA0040.10.584
MA0041.10.321
MA0042.10.774
MA0043.18.64978e-6
MA0046.10.385
MA0047.20.305
MA0048.10.996
MA0050.10.00512
MA0051.10.342
MA0052.10.59
MA0055.10.393
MA0057.10.0812
MA0058.10.538
MA0059.10.024
MA0060.15.22303e-6
MA0061.10.83
MA0062.23.69334e-4
MA0065.20.00276
MA0066.10.0385
MA0067.10.0503
MA0068.10.239
MA0069.10.335
MA0070.10.813
MA0071.10.0803
MA0072.10.636
MA0073.10.793
MA0074.10.626
MA0076.10.0313
MA0077.10.282
MA0078.10.959
MA0079.20.298
MA0080.22.10195e-5
MA0081.10.312
MA0083.10.17
MA0084.10.455
MA0087.10.869
MA0088.10.325
MA0090.10.0597
MA0091.10.00189
MA0092.10.0425
MA0093.10.601
MA0099.20.00196
MA0100.10.416
MA0101.10.186
MA0102.20.192
MA0103.10.469
MA0104.20.179
MA0105.10.119
MA0106.10.0239
MA0107.10.285
MA0108.20.0735
MA0111.10.95
MA0112.22.0665e-4
MA0113.10.00672
MA0114.10.0416
MA0115.10.582
MA0116.10.0227
MA0117.10.509
MA0119.10.02
MA0122.10.95
MA0124.10.0571
MA0125.10.519
MA0131.10.29
MA0135.10.838
MA0136.11.2235e-5
MA0137.20.144
MA0138.20.267
MA0139.10.535
MA0140.10.689
MA0141.10.044
MA0142.10.888
MA0143.10.442
MA0144.10.197
MA0145.10.146
MA0146.10.387
MA0147.10.0647
MA0148.10.141
MA0149.10.279
MA0150.10.41
MA0152.10.211
MA0153.10.112
MA0154.10.0945
MA0155.10.263
MA0156.11.37835e-4
MA0157.10.297
MA0159.10.126
MA0160.10.164
MA0162.10.123
MA0163.16.42947e-4
MA0164.10.649
MA0258.10.0335
MA0259.10.406



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: CNhs11371

Novel motifP-value
10.137
100.488
1000.749
1010.745
1020.4
1030.0956
1040.93
1050.0947
1060.0675
1070.0608
1080.482
1090.285
110.121
1100.195
1110.324
1120.0895
1130.199
1140.117
1150.055
1160.17
1170.594
1180.789
1190.706
120.672
1200.539
1210.688
1220.159
1230.152
1240.378
1250.637
1260.658
1270.249
1280.118
1290.317
130.712
1300.488
1310.368
1320.599
1330.538
1340.289
1350.119
1360.568
1370.914
1380.886
1390.06
140.457
1400.76
1410.942
1420.751
1430.0932
1440.274
1450.33
1460.362
1470.302
1480.141
1490.04
150.31
1500.509
1510.313
1520.229
1530.272
1540.676
1550.142
1560.423
1570.557
1580.134
1590.243
160.125
1600.0489
1610.571
1620.919
1630.96
1640.248
1650.942
1660.802
1670.877
1680.902
1690.00948
170.129
180.0153
190.0118
20.263
200.319
210.0347
220.138
230.0833
240.159
250.897
260.259
270.106
280.176
290.358
30.312
300.455
310.392
320.0054
330.634
340.388
350.321
360.722
370.0899
380.543
390.163
40.633
400.689
410.612
420.776
430.119
440.502
450.532
460.142
470.343
480.263
490.237
50.238
500.451
510.401
520.369
530.81
540.381
550.613
560.556
570.28
580.455
590.0685
60.558
600.386
610.496
620.182
630.118
640.413
650.202
660.583
670.323
680.23
690.217
70.629
700.0201
710.0616
720.403
730.119
740.0963
750.148
760.776
770.0032
780.877
790.112
80.0326
800.713
810.306
820.0733
830.923
840.414
850.0691
860.754
870.127
880.457
890.0293
90.269
900.755
910.365
920.041
930.92
940.154
950.763
960.701
970.98
980.0706
990.0424



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: CNhs11371


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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