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FF:11280-116I2: 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 16:39, 29 March 2012


Name:Preadipocyte - visceral, donor1
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 stage56 years old adult
sexfemale
age56
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 number2161
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-penis-0.0368
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-lymphoma0.386
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11082

Jaspar motifP-value
MA0002.20.128
MA0003.10.907
MA0004.10.755
MA0006.10.662
MA0007.10.868
MA0009.10.287
MA0014.10.533
MA0017.10.0787
MA0018.24.43136e-6
MA0019.10.608
MA0024.10.00201
MA0025.10.0154
MA0027.10.86
MA0028.10.215
MA0029.10.398
MA0030.10.0455
MA0031.10.0233
MA0035.20.00492
MA0038.10.762
MA0039.20.0671
MA0040.10.947
MA0041.10.966
MA0042.10.771
MA0043.11.02318e-4
MA0046.10.818
MA0047.20.49
MA0048.10.0146
MA0050.10.257
MA0051.10.346
MA0052.10.248
MA0055.10.813
MA0057.10.514
MA0058.10.876
MA0059.10.323
MA0060.10.0395
MA0061.10.162
MA0062.20.0603
MA0065.20.0421
MA0066.10.821
MA0067.10.0208
MA0068.10.871
MA0069.10.172
MA0070.10.447
MA0071.10.712
MA0072.10.244
MA0073.10.981
MA0074.10.704
MA0076.10.367
MA0077.10.302
MA0078.10.333
MA0079.20.719
MA0080.24.81141e-7
MA0081.10.16
MA0083.10.0156
MA0084.10.169
MA0087.10.942
MA0088.10.14
MA0090.10.00109
MA0091.10.145
MA0092.10.258
MA0093.10.971
MA0099.27.91443e-5
MA0100.10.0582
MA0101.10.0424
MA0102.20.163
MA0103.11.01663e-6
MA0104.20.836
MA0105.10.997
MA0106.10.279
MA0107.10.0275
MA0108.20.0434
MA0111.10.616
MA0112.20.817
MA0113.10.797
MA0114.10.0459
MA0115.10.395
MA0116.10.409
MA0117.10.349
MA0119.10.239
MA0122.10.199
MA0124.10.49
MA0125.10.885
MA0131.10.915
MA0135.10.349
MA0136.15.8631e-4
MA0137.20.104
MA0138.20.323
MA0139.10.438
MA0140.10.066
MA0141.10.389
MA0142.10.36
MA0143.10.794
MA0144.10.391
MA0145.10.579
MA0146.10.202
MA0147.10.687
MA0148.10.474
MA0149.10.95
MA0150.10.716
MA0152.13.80978e-4
MA0153.10.352
MA0154.10.204
MA0155.10.284
MA0156.10.0087
MA0157.10.0759
MA0159.10.235
MA0160.10.0588
MA0162.10.583
MA0163.10.0818
MA0164.10.83
MA0258.10.0247
MA0259.10.651



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: CNhs11082

Novel motifP-value
10.747
100.358
1000.343
1010.956
1020.246
1030.722
1040.776
1050.292
1060.13
1070.397
1080.693
1090.883
110.691
1100.17
1110.628
1120.719
1133.85733e-4
1140.56
1150.618
1160.475
1170.771
1180.0449
1190.32
120.392
1200.736
1210.489
1220.00852
1230.00111
1240.788
1250.662
1260.17
1270.853
1280.697
1290.556
130.689
1300.0528
1310.922
1320.607
1330.216
1340.244
1350.968
1360.434
1370.768
1380.175
1390.0186
140.0565
1400.132
1410.569
1420.868
1430.932
1440.949
1450.803
1460.752
1470.071
1480.493
1490.916
150.259
1500.366
1510.178
1520.421
1530.776
1540.885
1550.00794
1560.382
1570.298
1586.26389e-4
1590.136
160.418
1600.653
1610.108
1620.445
1630.925
1640.951
1650.468
1660.811
1670.136
1680.569
1690.278
170.844
180.86
190.0729
20.313
200.225
210.0248
220.839
230.833
240.559
250.416
260.919
270.613
280.159
290.559
30.621
300.121
310.541
320.0606
330.638
340.992
350.0984
360.0576
370.744
380.401
390.101
40.155
400.00131
410.094
420.692
430.386
440.875
450.274
460.876
470.756
480.856
490.0732
50.541
500.438
510.863
520.616
530.181
540.693
550.223
560.887
570.445
580.283
590.819
60.572
600.303
610.931
620.598
630.894
640.417
650.532
660.445
670.921
680.961
690.402
70.237
700.11
710.545
720.756
730.708
740.108
750.479
760.153
770.325
780.132
790.505
80.722
800.971
810.683
820.158
830.753
840.704
850.132
860.659
870.372
880.844
890.725
90.145
900.308
910.813
920.83
930.3
940.932
950.135
960.858
970.648
980.0936
990.0016



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: CNhs11082


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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