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FF:11428-118G6: 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 17:08, 29 March 2012


Name:Preadipocyte - 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 stage60 years old adult
sexfemale
age60
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 number1634
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-penis0.0355
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-lymphoma0.117
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12038

Jaspar motifP-value
MA0002.20.945
MA0003.10.222
MA0004.10.487
MA0006.10.188
MA0007.10.265
MA0009.10.235
MA0014.10.53
MA0017.10.941
MA0018.21.01258e-5
MA0019.10.486
MA0024.10.15
MA0025.10.0698
MA0027.10.855
MA0028.10.138
MA0029.10.326
MA0030.10.00518
MA0031.10.00464
MA0035.20.105
MA0038.10.00724
MA0039.20.0378
MA0040.10.621
MA0041.10.584
MA0042.10.946
MA0043.15.48076e-6
MA0046.10.715
MA0047.20.402
MA0048.10.177
MA0050.10.0234
MA0051.10.201
MA0052.10.306
MA0055.10.614
MA0057.10.0915
MA0058.10.301
MA0059.10.224
MA0060.12.43179e-5
MA0061.10.727
MA0062.29.91757e-5
MA0065.20.877
MA0066.10.403
MA0067.10.00564
MA0068.10.377
MA0069.10.218
MA0070.10.222
MA0071.10.515
MA0072.10.589
MA0073.10.886
MA0074.10.118
MA0076.10.0408
MA0077.10.325
MA0078.10.702
MA0079.20.716
MA0080.21.20166e-6
MA0081.10.0413
MA0083.10.0045
MA0084.10.752
MA0087.10.593
MA0088.10.523
MA0090.10.0261
MA0091.10.0153
MA0092.10.176
MA0093.10.546
MA0099.20.363
MA0100.10.4
MA0101.10.0356
MA0102.20.0576
MA0103.10.0311
MA0104.20.425
MA0105.10.784
MA0106.10.0106
MA0107.10.0911
MA0108.20.0106
MA0111.10.624
MA0112.20.0084
MA0113.10.565
MA0114.10.474
MA0115.10.644
MA0116.10.232
MA0117.10.459
MA0119.10.405
MA0122.10.344
MA0124.10.334
MA0125.10.0824
MA0131.10.212
MA0135.10.796
MA0136.16.04657e-8
MA0137.20.372
MA0138.20.179
MA0139.10.795
MA0140.10.138
MA0141.10.223
MA0142.10.613
MA0143.10.851
MA0144.10.951
MA0145.10.277
MA0146.10.344
MA0147.11
MA0148.10.485
MA0149.10.624
MA0150.10.378
MA0152.10.0344
MA0153.10.818
MA0154.10.445
MA0155.10.342
MA0156.11.37882e-5
MA0157.10.0298
MA0159.10.888
MA0160.10.723
MA0162.10.294
MA0163.10.0015
MA0164.10.711
MA0258.10.35
MA0259.10.698



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: CNhs12038

Novel motifP-value
10.663
100.777
1000.858
1010.498
1020.601
1030.187
1040.71
1050.184
1060.0579
1070.0302
1080.179
1090.14
110.43
1100.253
1110.622
1120.186
1130.00529
1140.326
1150.0342
1160.0551
1170.635
1180.661
1190.747
120.477
1200.146
1210.726
1220.062
1230.00413
1240.54
1250.292
1260.53
1270.625
1280.0905
1290.592
130.984
1300.56
1310.806
1320.486
1330.197
1340.357
1350.877
1360.937
1370.658
1380.471
1390.7
140.141
1400.707
1410.954
1420.685
1430.0665
1440.988
1450.97
1460.931
1470.159
1480.577
1490.0506
150.83
1500.0662
1510.496
1520.00701
1530.885
1540.449
1550.158
1560.396
1570.6
1580.0134
1590.309
160.0138
1600.306
1610.513
1620.173
1630.681
1640.206
1650.748
1660.629
1670.673
1680.985
1690.0167
170.209
180.151
190.0159
20.161
200.243
210.047
220.147
230.546
240.789
250.313
260.18
270.181
280.117
290.358
30.501
300.255
310.732
324.45017e-11
330.936
340.557
350.645
360.0377
370.0918
380.906
390.134
40.911
400.336
410.676
420.753
430.579
440.0763
450.799
460.211
470.876
480.523
490.815
50.862
500.496
510.441
520.76
530.211
540.674
550.454
560.996
570.79
580.482
590.0454
60.692
600.716
610.816
620.748
630.424
640.71
650.205
660.605
670.516
680.458
690.246
70.337
700.442
710.136
720.923
730.0123
740.0778
750.241
760.63
770.0169
780.508
790.0115
80.0644
800.579
810.807
820.528
830.533
840.459
850.351
860.585
870.017
880.571
890.0433
90.138
900.342
910.463
920.361
930.677
940.642
950.0168
960.963
970.635
980.362
990.00205



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: CNhs12038


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)
0002583 (subcutaneous preadipocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002072 (hypodermis)
0002199 (integument)
0002384 (connective tissue)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004120 (mesoderm-derived structure)
0005423 (developing anatomical structure)

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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