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FF:11376-118A8: 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 16:37, 29 March 2012


Name:Adipocyte - breast, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebreast
dev stage52 years old adult
sexfemale
age52
cell typeadipocyte
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-0.0662
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-0.336
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: CNhs11051

Jaspar motifP-value
MA0002.20.241
MA0003.10.401
MA0004.10.302
MA0006.10.116
MA0007.10.297
MA0009.10.207
MA0014.10.307
MA0017.10.489
MA0018.21.6224e-5
MA0019.10.383
MA0024.11.82728e-6
MA0025.15.63121e-4
MA0027.10.665
MA0028.10.0793
MA0029.10.252
MA0030.10.496
MA0031.10.95
MA0035.20.0273
MA0038.10.0129
MA0039.20.00311
MA0040.10.413
MA0041.10.608
MA0042.10.803
MA0043.12.76212e-4
MA0046.10.467
MA0047.20.373
MA0048.10.407
MA0050.11.68309e-4
MA0051.10.117
MA0052.10.603
MA0055.10.815
MA0057.10.506
MA0058.10.173
MA0059.10.714
MA0060.14.77732e-10
MA0061.13.33417e-4
MA0062.21.6785e-6
MA0065.20.203
MA0066.10.607
MA0067.10.11
MA0068.10.125
MA0069.10.0742
MA0070.10.652
MA0071.10.94
MA0072.10.586
MA0073.10.962
MA0074.10.974
MA0076.10.00341
MA0077.10.462
MA0078.10.579
MA0079.20.95
MA0080.22.84339e-6
MA0081.10.0428
MA0083.10.00505
MA0084.10.192
MA0087.10.321
MA0088.10.855
MA0090.17.68396e-8
MA0091.10.088
MA0092.10.0101
MA0093.10.228
MA0099.21.79812e-4
MA0100.10.892
MA0101.13.872e-7
MA0102.20.332
MA0103.13.78712e-5
MA0104.20.0057
MA0105.10.0259
MA0106.10.31
MA0107.19.11314e-7
MA0108.20.0516
MA0111.10.709
MA0112.20.00635
MA0113.10.0247
MA0114.10.614
MA0115.10.00248
MA0116.10.887
MA0117.10.272
MA0119.10.121
MA0122.10.647
MA0124.10.301
MA0125.10.662
MA0131.10.227
MA0135.10.114
MA0136.11.9298e-8
MA0137.20.859
MA0138.20.251
MA0139.10.341
MA0140.10.256
MA0141.10.708
MA0142.10.101
MA0143.10.923
MA0144.10.586
MA0145.10.172
MA0146.10.771
MA0147.10.0211
MA0148.10.34
MA0149.10.544
MA0150.10.0173
MA0152.10.00297
MA0153.10.88
MA0154.10.921
MA0155.10.321
MA0156.15.65679e-7
MA0157.10.518
MA0159.10.263
MA0160.10.109
MA0162.10.0886
MA0163.10.383
MA0164.10.883
MA0258.10.63
MA0259.10.219



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: CNhs11051

Novel motifP-value
10.747
100.713
1000.669
1010.198
1020.0174
1030.716
1040.616
1050.122
1060.114
1070.118
1080.439
1090.94
110.409
1100.848
1110.938
1120.705
1130.503
1140.198
1150.0416
1160.276
1170.262
1180.143
1190.501
120.369
1200.924
1210.678
1220.175
1230.0137
1240.558
1250.58
1260.556
1270.209
1280.64
1290.887
130.474
1300.372
1310.494
1320.345
1330.479
1340.331
1350.293
1360.708
1370.807
1380.186
1390.441
140.173
1400.527
1410.592
1420.56
1430.802
1440.775
1450.847
1460.85
1470.294
1480.913
1490.00215
150.764
1500.75
1510.904
1520.0125
1530.157
1540.807
1559.38888e-4
1560.197
1570.672
1580.0227
1590.483
160.0347
1600.579
1610.336
1620.557
1630.205
1640.756
1650.629
1660.325
1670.431
1680.894
1690.0411
170.849
180.402
190.0101
20.323
200.388
210.418
220.23
230.244
240.372
250.264
260.741
270.642
280.12
290.604
30.742
300.402
310.752
322.13856e-12
330.968
340.867
350.659
360.0804
370.198
380.538
390.129
40.581
400.113
410.898
420.344
430.366
440.721
450.802
460.969
470.723
480.663
490.994
50.608
500.647
510.679
520.558
530.106
540.751
550.152
560.677
570.948
580.438
590.212
60.423
600.859
610.257
620.532
630.561
640.23
650.761
660.152
670.66
680.516
690.652
70.277
700.999
710.52
720.712
730.01
740.148
750.957
760.611
770.0889
780.332
790.145
80.946
800.597
810.514
820.609
830.496
840.0843
850.0505
860.604
870.241
880.803
890.177
90.523
900.585
910.704
920.0804
930.902
940.938
950.433
960.564
970.271
980.58
990.0326



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: CNhs11051


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)
0002617 (adipocyte of breast)

UBERON: Anatomy
0000061 (anatomical structure)
0000310 (breast)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000915 (thoracic segment of trunk)
0001062 (anatomical entity)
0001443 (chest)
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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