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FF:12232-129F9: 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, donor2
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
age42
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-0.106
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-0.41
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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: CNhs12559

Jaspar motifP-value
MA0002.20.109
MA0003.10.564
MA0004.10.903
MA0006.10.813
MA0007.10.623
MA0009.10.085
MA0014.10.761
MA0017.10.229
MA0018.20.0186
MA0019.10.367
MA0024.10.0361
MA0025.13.87161e-5
MA0027.10.798
MA0028.10.0137
MA0029.10.767
MA0030.10.00303
MA0031.12.03164e-4
MA0035.20.979
MA0038.10.428
MA0039.20.235
MA0040.10.276
MA0041.10.00265
MA0042.10.0976
MA0043.17.64787e-5
MA0046.10.644
MA0047.20.00763
MA0048.10.762
MA0050.10.67
MA0051.10.112
MA0052.12.53475e-6
MA0055.10.216
MA0057.10.434
MA0058.10.931
MA0059.10.0666
MA0060.10.806
MA0061.10.879
MA0062.23.03817e-4
MA0065.20.243
MA0066.10.0249
MA0067.10.234
MA0068.11.19051e-5
MA0069.10.935
MA0070.10.296
MA0071.10.929
MA0072.10.0641
MA0073.10.829
MA0074.10.587
MA0076.10.0227
MA0077.10.355
MA0078.10.0634
MA0079.20.0393
MA0080.20.204
MA0081.10.592
MA0083.10.00872
MA0084.10.839
MA0087.10.676
MA0088.10.164
MA0090.10.00818
MA0091.10.247
MA0092.10.866
MA0093.10.919
MA0099.20.892
MA0100.10.762
MA0101.10.00382
MA0102.20.0181
MA0103.13.09037e-5
MA0104.20.0949
MA0105.19.0642e-4
MA0106.10.0737
MA0107.13.69157e-4
MA0108.22.68603e-11
MA0111.10.102
MA0112.20.015
MA0113.10.179
MA0114.10.0281
MA0115.10.573
MA0116.15.87901e-5
MA0117.10.996
MA0119.10.816
MA0122.10.156
MA0124.10.35
MA0125.10.486
MA0131.10.823
MA0135.10.302
MA0136.10.0593
MA0137.21.17459e-11
MA0138.20.845
MA0139.10.0218
MA0140.10.533
MA0141.10.289
MA0142.10.121
MA0143.10.528
MA0144.18.02679e-5
MA0145.10.309
MA0146.10.978
MA0147.10.0288
MA0148.10.0536
MA0149.10.979
MA0150.10.569
MA0152.10.208
MA0153.10.0382
MA0154.10.123
MA0155.10.95
MA0156.10.108
MA0157.10.00572
MA0159.10.334
MA0160.10.49
MA0162.10.534
MA0163.12.06959e-9
MA0164.10.892
MA0258.10.00842
MA0259.10.193



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: CNhs12559

Novel motifP-value
10.0935
100.109
1000.783
1010.476
1020.448
1030.174
1040.927
1050.974
1060.878
1070.687
1080.376
1090.121
110.127
1100.0518
1110.0258
1120.138
1130.783
1140.00712
1150.266
1160.0727
1170.00891
1180.132
1190.961
120.365
1200.0749
1210.828
1220.679
1230.0154
1240.546
1250.0725
1260.843
1270.102
1280.725
1290.684
130.631
1300.402
1310.278
1320.409
1330.871
1340.61
1350.703
1360.189
1370.921
1380.148
1390.565
140.759
1405.94193e-4
1410.242
1420.742
1430.0322
1440.699
1450.0742
1460.294
1470.751
1480.0786
1490.931
150.207
1500.581
1510.596
1520.247
1530.124
1540.245
1550.178
1560.219
1570.678
1580.312
1590.176
160.0968
1600.186
1610.138
1620.904
1630.73
1640.11
1650.466
1660.955
1670.275
1680.731
1690.469
170.325
180.0757
190.883
20.922
200.697
210.256
220.722
230.455
240.964
250.641
260.0478
270.337
280.755
290.0277
30.106
300.427
310.572
326.47694e-4
330.998
340.609
350.165
360.47
370.515
380.456
390.0845
40.287
400.466
410.989
420.368
430.346
440.0131
450.399
460.0234
470.054
480.069
490.0901
50.36
500.816
510.499
520.364
530.821
540.736
550.176
560.315
570.134
580.527
590.227
60.677
600.625
610.214
620.334
630.489
640.151
650.886
660.503
670.29
680.992
690.00219
70.854
700.0224
710.0273
720.866
730.907
740.583
750.101
760.294
770.66
780.837
790.116
80.151
800.186
810.225
820.705
830.18
840.91
850.743
860.737
870.4
880.815
890.302
90.382
900.564
910.412
920.8
930.661
940.112
950.196
960.904
970.335
980.459
990.597



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: CNhs12559


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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