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FF:11329-117E6: 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 17:00, 29 March 2012


Name:Preadipocyte - omental, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueomentum
dev stage24 years old adult
sexfemale
age24
cell typepreadipocyte
cell lineNA
companyZenbio
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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
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-0.165
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: CNhs11902

Jaspar motifP-value
MA0002.20.388
MA0003.10.452
MA0004.10.0589
MA0006.10.127
MA0007.10.987
MA0009.10.23
MA0014.10.231
MA0017.10.189
MA0018.27.27275e-5
MA0019.10.368
MA0024.14.82981e-6
MA0025.10.0119
MA0027.10.54
MA0028.10.0027
MA0029.10.617
MA0030.10.718
MA0031.10.746
MA0035.20.0425
MA0038.10.398
MA0039.20.0316
MA0040.10.134
MA0041.10.462
MA0042.10.505
MA0043.15.98475e-4
MA0046.10.441
MA0047.20.531
MA0048.10.458
MA0050.12.28252e-4
MA0051.10.0792
MA0052.10.888
MA0055.10.661
MA0057.10.397
MA0058.10.0332
MA0059.10.132
MA0060.18.19754e-6
MA0061.10.00355
MA0062.21.89351e-7
MA0065.20.0688
MA0066.10.782
MA0067.10.0545
MA0068.10.671
MA0069.10.0136
MA0070.10.866
MA0071.10.606
MA0072.10.814
MA0073.10.721
MA0074.10.748
MA0076.10.00212
MA0077.10.848
MA0078.10.909
MA0079.20.973
MA0080.22.81803e-5
MA0081.10.0504
MA0083.10.0069
MA0084.10.552
MA0087.10.619
MA0088.10.319
MA0090.11.10331e-6
MA0091.10.0843
MA0092.10.0202
MA0093.10.0636
MA0099.20.00862
MA0100.10.845
MA0101.15.18962e-5
MA0102.20.206
MA0103.11.22714e-4
MA0104.26.274e-4
MA0105.10.0127
MA0106.10.252
MA0107.14.77824e-4
MA0108.20.0129
MA0111.10.768
MA0112.20.0485
MA0113.10.333
MA0114.10.141
MA0115.10.0229
MA0116.10.714
MA0117.10.242
MA0119.10.93
MA0122.10.956
MA0124.10.712
MA0125.10.991
MA0131.10.205
MA0135.10.221
MA0136.11.37187e-7
MA0137.20.77
MA0138.20.521
MA0139.10.35
MA0140.10.565
MA0141.10.204
MA0142.10.615
MA0143.10.468
MA0144.10.657
MA0145.10.0708
MA0146.10.228
MA0147.10.00303
MA0148.10.868
MA0149.10.687
MA0150.10.0614
MA0152.10.00381
MA0153.10.933
MA0154.10.762
MA0155.10.14
MA0156.11.19366e-5
MA0157.10.952
MA0159.10.212
MA0160.10.0755
MA0162.10.116
MA0163.10.812
MA0164.10.721
MA0258.10.816
MA0259.10.0924



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: CNhs11902

Novel motifP-value
10.43
100.433
1000.352
1010.34
1020.0648
1030.514
1040.865
1050.162
1060.485
1070.191
1080.488
1090.271
110.334
1100.747
1110.871
1120.993
1130.629
1140.368
1150.126
1160.484
1170.0677
1180.0707
1190.404
120.121
1200.862
1210.747
1220.63
1230.0012
1240.639
1250.369
1260.816
1270.397
1280.7
1290.571
130.323
1300.543
1310.408
1320.481
1330.948
1340.212
1350.108
1360.409
1370.916
1380.859
1390.906
140.384
1400.744
1410.302
1420.913
1430.929
1440.933
1450.833
1460.841
1470.0891
1480.184
1490.00187
150.885
1500.986
1510.884
1520.0175
1530.247
1540.758
1550.00348
1560.639
1570.28
1580.0202
1590.773
160.0594
1600.735
1610.0453
1620.657
1630.43
1640.7
1650.813
1660.408
1670.365
1680.746
1690.126
170.796
180.203
190.0341
20.592
200.17
210.39
220.473
230.0904
240.214
250.346
260.547
270.563
280.226
290.232
30.932
300.156
310.851
324.90261e-11
330.359
340.67
350.449
360.129
370.872
380.466
390.292
40.655
400.438
410.767
420.505
430.904
440.556
450.623
460.895
470.388
480.371
490.974
50.469
500.888
510.842
520.498
530.0712
540.631
550.118
560.501
570.791
580.159
590.651
60.712
600.997
610.107
620.434
630.855
640.274
650.925
660.474
670.902
680.796
690.577
70.28
700.753
710.948
720.898
730.0521
740.438
750.389
760.13
770.143
780.0869
790.0244
80.908
800.87
810.572
820.757
830.906
840.0575
850.0493
860.584
870.814
880.664
890.46
90.229
900.92
910.692
920.238
930.44
940.768
950.461
960.232
970.209
980.389
990.0396



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: CNhs11902


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)
0002579 (omentum preadipocyte)

UBERON: Anatomy
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001178 (visceral peritoneum)
0002050 (embryonic structure)
0002100 (trunk)
0002323 (body cavity)
0002358 (peritoneum)
0002384 (connective tissue)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003684 (abdominal cavity)
0003688 (omentum)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004923 (organ component layer)
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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