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FF:11469-119C2: 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:Preadipocyte - perirenal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stage66 years old adult
sexfemale
age66
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-v1.1
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-0.0809
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
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: CNhs12065

Jaspar motifP-value
MA0002.20.45
MA0003.10.126
MA0004.10.872
MA0006.10.306
MA0007.10.0653
MA0009.10.679
MA0014.10.602
MA0017.10.271
MA0018.24.43325e-4
MA0019.10.911
MA0024.14.54829e-6
MA0025.10.00793
MA0027.10.899
MA0028.10.0194
MA0029.10.209
MA0030.10.652
MA0031.10.455
MA0035.20.947
MA0038.10.0122
MA0039.20.6
MA0040.10.353
MA0041.10.325
MA0042.10.819
MA0043.10.00318
MA0046.10.39
MA0047.20.668
MA0048.10.86
MA0050.12.70593e-6
MA0051.10.041
MA0052.10.793
MA0055.10.862
MA0057.10.0872
MA0058.10.979
MA0059.10.433
MA0060.14.25896e-6
MA0061.10.948
MA0062.23.30069e-5
MA0065.20.15
MA0066.10.0853
MA0067.10.0264
MA0068.10.121
MA0069.10.206
MA0070.10.841
MA0071.10.263
MA0072.10.961
MA0073.10.864
MA0074.10.465
MA0076.10.00386
MA0077.10.373
MA0078.10.151
MA0079.20.433
MA0080.21.4222e-5
MA0081.10.0219
MA0083.13.54579e-4
MA0084.10.97
MA0087.10.452
MA0088.10.639
MA0090.11.23107e-4
MA0091.10.0388
MA0092.10.0187
MA0093.10.978
MA0099.20.792
MA0100.10.382
MA0101.10.0795
MA0102.20.158
MA0103.10.986
MA0104.20.531
MA0105.10.679
MA0106.10.104
MA0107.10.159
MA0108.27.04029e-4
MA0111.10.792
MA0112.22.92432e-4
MA0113.10.0153
MA0114.10.285
MA0115.10.243
MA0116.10.113
MA0117.10.635
MA0119.10.0942
MA0122.10.725
MA0124.10.0141
MA0125.10.273
MA0131.10.125
MA0135.10.981
MA0136.11.74148e-8
MA0137.20.0739
MA0138.20.0694
MA0139.10.707
MA0140.10.865
MA0141.10.125
MA0142.10.121
MA0143.10.836
MA0144.10.686
MA0145.10.182
MA0146.10.16
MA0147.10.79
MA0148.10.415
MA0149.10.285
MA0150.10.782
MA0152.10.0548
MA0153.10.0268
MA0154.10.0857
MA0155.10.0784
MA0156.13.89134e-5
MA0157.10.601
MA0159.10.0331
MA0160.10.55
MA0162.10.0681
MA0163.10.00859
MA0164.10.722
MA0258.10.00504
MA0259.10.707



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: CNhs12065

Novel motifP-value
10.312
100.905
1000.59
1010.886
1020.579
1030.261
1040.32
1050.907
1060.0287
1070.0208
1080.229
1090.123
110.176
1100.312
1110.699
1120.353
1130.939
1140.0866
1150.105
1160.156
1170.859
1180.585
1190.395
120.662
1200.721
1210.74
1220.975
1230.268
1240.891
1250.939
1260.894
1270.702
1280.0671
1290.553
130.94
1300.607
1310.924
1320.853
1330.474
1340.44
1350.212
1360.88
1370.878
1380.858
1390.0124
140.978
1400.842
1410.782
1420.567
1430.083
1440.704
1450.821
1460.157
1470.209
1480.534
1490.00229
150.359
1500.539
1510.323
1520.0305
1530.59
1540.487
1550.624
1560.511
1570.95
1580.438
1590.953
160.0384
1600.112
1610.707
1620.875
1630.96
1640.343
1650.685
1660.497
1670.361
1680.165
1690.0148
170.113
180.0938
190.0626
20.203
200.506
210.981
220.0725
230.0494
240.72
250.725
260.203
270.0961
280.376
290.63
30.316
300.456
310.373
321.27741e-10
330.605
340.428
350.537
360.487
370.118
380.58
390.188
40.188
400.28
410.489
420.895
430.0894
440.134
450.407
460.206
470.49
480.37
490.23
50.26
500.557
510.497
520.258
530.899
540.317
550.338
560.682
570.302
580.819
590.0487
60.888
600.173
610.91
620.923
630.129
640.419
650.187
660.587
670.408
680.0767
690.129
70.715
700.057
710.381
720.955
730.0306
740.351
750.39
760.608
770.0144
780.913
790.00625
80.0779
800.88
810.565
820.0932
830.834
840.134
850.0151
860.588
870.399
880.231
890.00951
90.291
900.688
910.707
920.0382
930.825
940.33
950.179
960.823
970.189
980.346
990.0759



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: CNhs12065


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)
0002581 (perirenal preadipocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001013 (adipose tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0005406 (perirenal fat)

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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