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FF:12231-129F8: 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 17:21, 29 March 2012


Name:mature adipocyte, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueadipose tissue
dev stageNA
sexfemale
age43
cell typeadipocyte
cell lineNA
companyNA
collaborationPeter Arner (Karolinska Institutet)
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-v1.0
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-0.156
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-0.443
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs12558

Jaspar motifP-value
MA0002.20.0979
MA0003.10.91
MA0004.10.891
MA0006.10.84
MA0007.10.921
MA0009.10.0742
MA0014.10.969
MA0017.10.412
MA0018.20.014
MA0019.10.709
MA0024.10.0355
MA0025.16.02047e-6
MA0027.10.923
MA0028.16.08083e-4
MA0029.10.447
MA0030.10.00277
MA0031.12.19979e-4
MA0035.20.791
MA0038.10.21
MA0039.20.326
MA0040.10.173
MA0041.10.098
MA0042.10.103
MA0043.16.54459e-6
MA0046.10.834
MA0047.20.00168
MA0048.10.927
MA0050.10.716
MA0051.10.508
MA0052.11.02953e-7
MA0055.10.453
MA0057.10.45
MA0058.10.985
MA0059.10.0658
MA0060.10.875
MA0061.10.402
MA0062.24.06984e-6
MA0065.20.452
MA0066.10.0361
MA0067.10.223
MA0068.16.16907e-6
MA0069.10.473
MA0070.10.479
MA0071.10.664
MA0072.10.0439
MA0073.10.863
MA0074.10.578
MA0076.12.61614e-4
MA0077.10.103
MA0078.10.0419
MA0079.20.0637
MA0080.20.028
MA0081.10.332
MA0083.10.00559
MA0084.10.71
MA0087.10.694
MA0088.10.142
MA0090.10.0668
MA0091.10.141
MA0092.10.971
MA0093.10.844
MA0099.20.105
MA0100.10.677
MA0101.10.011
MA0102.20.0286
MA0103.12.5493e-5
MA0104.20.0974
MA0105.19.9744e-5
MA0106.10.0968
MA0107.10.00405
MA0108.22.37051e-13
MA0111.10.224
MA0112.20.00927
MA0113.10.114
MA0114.10.0181
MA0115.10.445
MA0116.17.19968e-5
MA0117.10.871
MA0119.10.984
MA0122.10.183
MA0124.10.217
MA0125.10.72
MA0131.10.722
MA0135.10.26
MA0136.10.00345
MA0137.23.09333e-9
MA0138.20.939
MA0139.10.0156
MA0140.10.862
MA0141.10.494
MA0142.10.377
MA0143.10.687
MA0144.14.11533e-4
MA0145.10.615
MA0146.10.877
MA0147.10.0405
MA0148.10.023
MA0149.10.872
MA0150.10.544
MA0152.10.292
MA0153.10.0329
MA0154.10.0932
MA0155.10.831
MA0156.10.00146
MA0157.10.00631
MA0159.10.241
MA0160.10.222
MA0162.10.348
MA0163.15.7438e-10
MA0164.10.963
MA0258.10.0186
MA0259.10.221



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: CNhs12558

Novel motifP-value
10.0947
100.15
1000.668
1010.779
1020.227
1030.11
1040.997
1050.654
1060.915
1070.936
1080.432
1090.0495
110.107
1100.0906
1110.0526
1120.269
1130.556
1140.00163
1150.0922
1160.0503
1170.00923
1180.126
1190.715
120.299
1200.0404
1210.714
1220.865
1230.253
1240.327
1250.0718
1260.802
1270.129
1280.958
1290.995
130.424
1300.476
1310.588
1320.268
1330.377
1340.339
1350.488
1360.166
1370.904
1380.105
1390.56
140.891
1401.56862e-4
1410.246
1420.77
1430.0195
1440.847
1450.373
1460.452
1470.598
1480.0217
1490.32
150.298
1500.595
1510.462
1520.533
1530.0695
1540.495
1550.271
1560.287
1570.927
1580.506
1590.316
160.0526
1600.282
1610.0915
1620.554
1630.589
1640.203
1650.621
1660.662
1670.568
1680.781
1690.348
170.437
180.051
190.911
20.997
200.791
210.13
220.819
230.655
240.72
250.66
260.0819
270.303
280.729
290.0337
30.114
300.563
310.605
321.87908e-4
330.598
340.629
350.0842
360.169
370.222
380.456
390.092
40.18
400.332
410.929
420.404
430.312
440.00189
450.465
460.036
470.0457
480.0518
490.175
50.296
500.99
510.656
520.212
530.904
540.977
550.128
560.342
570.344
580.603
590.138
60.576
600.558
610.193
620.233
630.416
640.118
650.848
660.709
670.239
680.811
690.00232
70.66
700.00922
710.0153
720.938
730.519
740.731
750.0663
760.438
770.333
780.732
790.113
80.216
800.342
810.272
820.244
830.0561
840.879
850.932
860.44
870.259
880.811
890.136
90.662
900.755
910.422
920.924
930.489
940.0895
950.0692
960.981
970.346
980.442
990.512



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: CNhs12558


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)

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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