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FF:11429-118G7: 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 - visceral, donor3
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 stage51 years old adult
sexfemale
age51
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 number1851
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-0.0168
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-lymphoma0.291
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
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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: CNhs12039

Jaspar motifP-value
MA0002.20.518
MA0003.10.212
MA0004.10.739
MA0006.10.401
MA0007.10.22
MA0009.10.547
MA0014.10.562
MA0017.10.825
MA0018.27.93063e-5
MA0019.10.182
MA0024.10.274
MA0025.10.0798
MA0027.10.84
MA0028.10.783
MA0029.10.366
MA0030.10.00137
MA0031.10.00108
MA0035.20.0214
MA0038.10.0385
MA0039.20.0742
MA0040.10.901
MA0041.10.756
MA0042.10.657
MA0043.16.01815e-6
MA0046.10.514
MA0047.20.196
MA0048.10.0397
MA0050.10.767
MA0051.10.695
MA0052.10.24
MA0055.10.182
MA0057.10.157
MA0058.10.59
MA0059.10.134
MA0060.12.92871e-5
MA0061.10.941
MA0062.20.00852
MA0065.20.952
MA0066.10.371
MA0067.10.0298
MA0068.10.988
MA0069.10.359
MA0070.10.391
MA0071.10.337
MA0072.10.407
MA0073.10.958
MA0074.10.168
MA0076.10.403
MA0077.10.348
MA0078.10.819
MA0079.20.939
MA0080.21.39948e-6
MA0081.10.0937
MA0083.10.00645
MA0084.10.329
MA0087.10.89
MA0088.10.0668
MA0090.10.12
MA0091.10.0575
MA0092.10.374
MA0093.10.745
MA0099.20.352
MA0100.10.693
MA0101.10.0348
MA0102.20.00303
MA0103.10.00288
MA0104.20.89
MA0105.10.34
MA0106.10.0486
MA0107.10.0728
MA0108.20.0576
MA0111.10.512
MA0112.20.0202
MA0113.10.648
MA0114.10.261
MA0115.10.635
MA0116.10.033
MA0117.10.378
MA0119.10.329
MA0122.10.232
MA0124.10.141
MA0125.10.231
MA0131.10.417
MA0135.10.356
MA0136.12.28775e-6
MA0137.20.713
MA0138.20.34
MA0139.10.955
MA0140.10.0511
MA0141.10.116
MA0142.10.393
MA0143.10.757
MA0144.10.722
MA0145.10.425
MA0146.10.461
MA0147.10.522
MA0148.10.291
MA0149.10.794
MA0150.10.435
MA0152.10.0144
MA0153.10.145
MA0154.10.398
MA0155.10.54
MA0156.13.46641e-5
MA0157.10.047
MA0159.10.916
MA0160.10.7
MA0162.10.156
MA0163.10.0029
MA0164.10.826
MA0258.10.842
MA0259.10.726



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: CNhs12039

Novel motifP-value
10.514
100.217
1000.928
1010.233
1020.684
1030.265
1040.911
1050.233
1060.542
1070.183
1080.355
1090.0731
110.235
1100.045
1110.804
1120.108
1130.00689
1140.529
1150.00672
1160.0271
1170.255
1180.935
1190.737
120.455
1200.0973
1210.919
1220.019
1230.00953
1240.566
1250.265
1260.711
1270.731
1280.649
1290.973
130.845
1300.402
1310.288
1320.42
1330.0767
1340.731
1350.904
1360.292
1370.531
1380.567
1390.358
140.0783
1400.545
1410.896
1420.769
1430.213
1440.969
1450.686
1460.424
1470.0552
1480.59
1490.142
150.574
1500.108
1510.799
1520.0187
1530.423
1540.638
1550.237
1560.758
1570.373
1580.00853
1590.169
160.0286
1600.154
1610.522
1620.694
1630.45
1640.253
1650.53
1660.379
1670.368
1680.823
1690.0244
170.271
180.296
190.0198
20.116
200.503
210.0163
220.264
230.597
240.96
250.514
260.259
270.116
280.0869
290.1
30.372
300.181
310.85
323.93155e-8
330.993
340.525
350.71
360.0161
370.0494
380.954
390.0944
40.282
400.143
410.177
420.903
430.78
440.0103
450.972
460.241
470.649
480.483
490.288
50.593
500.447
510.595
520.831
530.116
540.722
550.509
560.89
570.72
580.61
590.0194
60.412
600.905
610.802
620.477
630.631
640.766
650.299
660.509
670.504
680.726
690.2
70.402
700.929
710.167
720.718
730.00925
740.144
750.14
760.819
770.00265
780.471
790.0203
80.046
800.492
810.997
820.658
830.745
840.683
850.78
860.576
870.00747
880.565
890.0645
90.162
900.135
910.831
920.524
930.758
940.666
950.00269
960.393
970.999
980.671
990.0047



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: CNhs12039


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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