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FF:11468-119C1: 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 16:38, 29 March 2012


Name:Preadipocyte - omental, donor1
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 stage58 years old adult
sexfemale
age58
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-penis-0.0935
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-0.407
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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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: CNhs11065

Jaspar motifP-value
MA0002.20.241
MA0003.10.531
MA0004.10.232
MA0006.10.211
MA0007.10.806
MA0009.10.138
MA0014.10.155
MA0017.10.247
MA0018.21.44911e-4
MA0019.10.841
MA0024.11.52337e-7
MA0025.10.0262
MA0027.10.387
MA0028.10.0818
MA0029.10.522
MA0030.10.812
MA0031.10.971
MA0035.20.0842
MA0038.10.00299
MA0039.20.0059
MA0040.10.239
MA0041.10.578
MA0042.10.704
MA0043.10.00608
MA0046.10.312
MA0047.20.971
MA0048.10.992
MA0050.10.00522
MA0051.10.392
MA0052.10.391
MA0055.10.372
MA0057.10.688
MA0058.10.169
MA0059.10.399
MA0060.18.34837e-13
MA0061.15.88221e-5
MA0062.24.84771e-6
MA0065.20.126
MA0066.10.645
MA0067.10.0448
MA0068.10.674
MA0069.10.0826
MA0070.10.523
MA0071.10.951
MA0072.10.398
MA0073.10.958
MA0074.10.891
MA0076.10.0174
MA0077.10.382
MA0078.10.849
MA0079.20.54
MA0080.21.50554e-6
MA0081.10.00555
MA0083.10.206
MA0084.10.475
MA0087.10.451
MA0088.10.299
MA0090.18.79672e-8
MA0091.10.0552
MA0092.10.0443
MA0093.10.277
MA0099.23.99293e-4
MA0100.10.541
MA0101.13.0021e-7
MA0102.20.351
MA0103.15.07916e-4
MA0104.20.00305
MA0105.13.76727e-4
MA0106.10.258
MA0107.11.85714e-6
MA0108.20.383
MA0111.10.377
MA0112.20.0956
MA0113.10.161
MA0114.10.183
MA0115.10.00964
MA0116.10.729
MA0117.10.401
MA0119.10.807
MA0122.10.561
MA0124.10.129
MA0125.10.367
MA0131.10.373
MA0135.10.224
MA0136.12.23597e-9
MA0137.20.949
MA0138.20.65
MA0139.10.427
MA0140.10.796
MA0141.10.542
MA0142.10.00849
MA0143.10.845
MA0144.10.671
MA0145.10.265
MA0146.10.524
MA0147.10.0108
MA0148.10.739
MA0149.10.561
MA0150.10.117
MA0152.10.00641
MA0153.10.494
MA0154.10.636
MA0155.10.362
MA0156.11.7388e-6
MA0157.10.744
MA0159.10.306
MA0160.10.0248
MA0162.10.0831
MA0163.10.647
MA0164.10.531
MA0258.10.868
MA0259.10.309



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: CNhs11065

Novel motifP-value
10.459
100.723
1000.606
1010.411
1020.0331
1030.655
1040.943
1050.134
1060.579
1070.486
1080.391
1090.632
110.353
1100.649
1110.752
1120.879
1130.0124
1140.152
1150.122
1160.222
1170.395
1180.146
1190.212
120.428
1200.689
1210.704
1220.299
1230.00137
1240.341
1250.123
1260.299
1270.124
1280.807
1290.975
130.247
1300.702
1310.114
1320.862
1330.265
1340.53
1350.686
1360.727
1370.897
1380.258
1390.411
140.209
1400.39
1410.784
1420.454
1430.844
1440.715
1450.115
1460.317
1470.135
1480.666
1498.6522e-5
150.899
1500.606
1510.874
1520.0206
1530.0679
1540.683
1550.00568
1560.306
1570.839
1580.0073
1590.379
160.013
1600.467
1610.261
1620.983
1630.0442
1640.61
1650.919
1660.0657
1670.379
1680.432
1690.0908
170.866
180.158
190.0258
20.342
200.351
210.32
220.225
230.268
240.0535
250.284
260.397
270.668
280.217
290.487
30.854
300.378
310.762
328.40543e-16
330.927
340.939
350.726
360.0276
370.461
380.17
390.22
40.559
400.191
410.694
420.205
430.963
440.692
450.948
460.721
470.405
480.492
490.483
50.394
500.846
510.459
520.712
530.0765
540.89
550.224
560.402
570.674
580.279
590.373
60.444
600.983
610.346
620.504
630.989
640.213
650.827
660.239
670.546
680.899
690.423
70.201
700.464
710.978
720.948
730.0262
740.283
750.746
760.438
770.134
780.1
790.0235
80.815
800.511
810.675
820.395
830.996
840.275
850.0912
860.37
870.194
880.605
890.342
90.547
900.871
910.494
920.135
930.76
940.929
950.835
960.823
970.264
980.179
990.152



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: CNhs11065


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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