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FF:11475-119C8: 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 17:10, 29 March 2012


Name:Adipocyte - omental, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.7
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-penis0.0428
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-0.44
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12068

Jaspar motifP-value
MA0002.20.146
MA0003.10.0938
MA0004.10.567
MA0006.10.201
MA0007.10.106
MA0009.10.209
MA0014.10.63
MA0017.10.801
MA0018.21.48979e-4
MA0019.10.231
MA0024.14.06575e-7
MA0025.10.00629
MA0027.10.275
MA0028.10.0232
MA0029.10.609
MA0030.10.148
MA0031.10.407
MA0035.20.338
MA0038.10.0822
MA0039.20.0375
MA0040.10.135
MA0041.10.269
MA0042.10.605
MA0043.10.00474
MA0046.10.167
MA0047.20.862
MA0048.10.724
MA0050.11.11013e-5
MA0051.10.012
MA0052.10.293
MA0055.10.841
MA0057.10.388
MA0058.10.593
MA0059.10.803
MA0060.11.00854e-6
MA0061.10.0532
MA0062.21.03187e-7
MA0065.20.101
MA0066.10.26
MA0067.10.0395
MA0068.10.688
MA0069.10.0761
MA0070.10.94
MA0071.10.0523
MA0072.10.497
MA0073.10.903
MA0074.10.429
MA0076.14.519e-4
MA0077.10.133
MA0078.10.916
MA0079.20.328
MA0080.22.50237e-7
MA0081.10.00494
MA0083.12.85159e-4
MA0084.10.857
MA0087.10.738
MA0088.10.92
MA0090.14.09086e-5
MA0091.10.0126
MA0092.10.0527
MA0093.10.455
MA0099.21.21868e-9
MA0100.10.422
MA0101.18.67926e-5
MA0102.20.102
MA0103.10.00611
MA0104.20.116
MA0105.10.274
MA0106.10.329
MA0107.11.11922e-4
MA0108.20.0454
MA0111.10.722
MA0112.25.59148e-4
MA0113.10.0202
MA0114.10.33
MA0115.10.0316
MA0116.10.885
MA0117.10.353
MA0119.10.236
MA0122.10.389
MA0124.10.0408
MA0125.10.263
MA0131.10.102
MA0135.10.913
MA0136.14.20809e-12
MA0137.20.929
MA0138.20.00849
MA0139.10.786
MA0140.10.446
MA0141.10.331
MA0142.10.0434
MA0143.10.749
MA0144.10.456
MA0145.10.0853
MA0146.10.223
MA0147.10.183
MA0148.10.571
MA0149.10.462
MA0150.10.0176
MA0152.10.0167
MA0153.10.594
MA0154.10.334
MA0155.10.0388
MA0156.13.6599e-11
MA0157.10.853
MA0159.10.241
MA0160.10.99
MA0162.10.0324
MA0163.10.08
MA0164.10.813
MA0258.10.148
MA0259.10.276



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: CNhs12068

Novel motifP-value
10.856
100.842
1000.7
1010.267
1020.0512
1030.602
1040.768
1050.186
1060.182
1070.111
1080.327
1090.638
110.649
1100.614
1110.66
1120.207
1130.723
1140.518
1150.00808
1160.0649
1170.605
1180.564
1190.547
120.728
1200.673
1210.657
1220.36
1230.0599
1240.927
1250.0573
1260.783
1270.41
1280.231
1290.492
130.997
1300.885
1310.893
1320.39
1330.447
1340.456
1350.691
1360.234
1370.406
1380.7
1390.425
140.458
1400.084
1410.611
1420.6
1430.858
1440.903
1450.279
1460.96
1470.319
1480.562
1491.47989e-4
150.688
1500.674
1510.785
1520.0845
1530.761
1540.338
1550.0497
1560.168
1570.968
1580.0376
1590.754
160.00896
1600.37
1610.557
1620.583
1630.474
1640.192
1650.491
1660.0916
1670.316
1680.749
1690.018
170.469
180.385
190.00202
20.128
200.264
210.671
220.0504
230.12
240.403
250.429
260.94
270.275
280.152
290.781
30.772
300.155
310.335
329.69114e-15
330.661
340.596
350.566
360.0983
370.117
380.982
390.108
40.74
400.8
410.84
420.21
430.274
440.233
450.655
460.889
470.723
480.946
490.876
50.636
500.565
510.981
520.39
530.181
540.953
550.394
560.467
570.966
580.876
590.0761
60.721
600.348
610.556
620.761
630.313
640.865
650.176
660.0427
670.452
680.48
690.705
70.857
700.895
710.465
720.28
730.0304
740.623
750.776
760.494
770.00319
780.914
790.0541
80.42
800.456
810.469
820.307
830.483
840.21
850.00918
860.372
870.194
880.773
890.114
90.445
900.936
910.456
920.116
930.589
940.594
950.734
960.894
970.368
980.841
990.0233



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: CNhs12068


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)
0000134 (mesenchymal cell)
0000136 (fat cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002615 (adipocyte of omentum tissue)

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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