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FF:11356-117H6: 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 - 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 stage53 years old adult
sexfemale
age53
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 number1377
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-penis0.131
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-lymphoma0.391
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11981

Jaspar motifP-value
MA0002.20.351
MA0003.10.699
MA0004.10.654
MA0006.10.383
MA0007.10.323
MA0009.10.775
MA0014.10.296
MA0017.10.734
MA0018.25.49942e-7
MA0019.10.727
MA0024.10.0726
MA0025.10.00723
MA0027.10.673
MA0028.10.589
MA0029.10.675
MA0030.16.85814e-5
MA0031.16.18151e-4
MA0035.20.00634
MA0038.10.0385
MA0039.20.0368
MA0040.10.546
MA0041.10.696
MA0042.10.343
MA0043.12.1506e-9
MA0046.10.312
MA0047.20.164
MA0048.10.0207
MA0050.10.879
MA0051.10.915
MA0052.10.0419
MA0055.10.102
MA0057.10.225
MA0058.10.388
MA0059.10.0311
MA0060.10.00129
MA0061.10.608
MA0062.20.0172
MA0065.20.717
MA0066.10.339
MA0067.16.48901e-4
MA0068.10.0649
MA0069.10.107
MA0070.10.304
MA0071.10.702
MA0072.10.315
MA0073.10.834
MA0074.10.285
MA0076.10.658
MA0077.10.459
MA0078.10.919
MA0079.20.267
MA0080.23.91284e-7
MA0081.10.0537
MA0083.10.0609
MA0084.10.478
MA0087.10.304
MA0088.10.0115
MA0090.10.399
MA0091.10.0556
MA0092.10.266
MA0093.10.666
MA0099.20.937
MA0100.10.379
MA0101.10.189
MA0102.20.00358
MA0103.10.00556
MA0104.20.627
MA0105.10.00797
MA0106.10.0214
MA0107.10.179
MA0108.20.572
MA0111.10.992
MA0112.20.008
MA0113.10.748
MA0114.10.803
MA0115.10.921
MA0116.10.0149
MA0117.10.821
MA0119.10.0391
MA0122.10.116
MA0124.10.73
MA0125.10.24
MA0131.10.669
MA0135.10.386
MA0136.11.68972e-5
MA0137.20.429
MA0138.20.743
MA0139.10.846
MA0140.10.0921
MA0141.10.522
MA0142.10.984
MA0143.10.862
MA0144.10.858
MA0145.10.656
MA0146.10.398
MA0147.10.186
MA0148.10.25
MA0149.10.379
MA0150.10.16
MA0152.10.0502
MA0153.10.0534
MA0154.10.188
MA0155.10.923
MA0156.17.34047e-5
MA0157.10.0231
MA0159.10.739
MA0160.10.225
MA0162.10.27
MA0163.12.674e-6
MA0164.10.876
MA0258.10.607
MA0259.10.728



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: CNhs11981

Novel motifP-value
10.176
100.0311
1000.76
1010.628
1020.805
1030.187
1040.82
1050.231
1060.162
1070.101
1080.418
1090.178
110.217
1100.0539
1110.211
1120.282
1130.00382
1140.368
1150.0163
1160.0249
1170.064
1180.941
1190.673
120.429
1200.0436
1210.858
1220.0129
1230.0575
1240.881
1250.1
1260.715
1270.799
1280.308
1290.902
130.676
1300.558
1310.16
1320.651
1330.0609
1340.983
1350.561
1360.78
1370.522
1380.426
1390.203
140.0846
1400.75
1410.598
1420.545
1430.103
1440.835
1450.575
1460.501
1470.0771
1480.0769
1490.163
150.998
1500.0714
1510.829
1520.0411
1530.829
1540.827
1550.0875
1560.744
1570.32
1580.00968
1590.315
160.0337
1600.0991
1610.39
1620.185
1630.795
1640.121
1650.75
1660.572
1670.747
1680.841
1690.0339
170.256
180.119
190.0182
20.268
200.579
210.00489
220.419
230.92
240.619
250.463
260.0685
270.235
280.176
290.0424
30.196
300.547
310.951
327.27825e-5
330.621
340.925
350.591
360.143
370.0753
380.882
390.211
40.896
400.149
410.26
420.614
430.626
440.0109
450.375
460.0728
470.301
480.27
490.91
50.695
500.643
510.583
520.8
530.358
540.947
550.583
560.687
570.885
580.656
590.0917
60.632
600.942
610.649
620.462
630.522
640.649
650.439
660.778
670.532
680.882
690.321
70.673
700.866
710.0401
720.961
730.0317
740.0167
750.0326
760.795
770.0471
780.989
790.0145
80.0442
800.158
810.732
820.645
830.161
840.558
850.689
860.568
870.0591
880.863
890.0657
90.289
900.76
910.862
920.619
930.626
940.571
950.0144
960.959
970.761
980.445
990.002



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: CNhs11981


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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