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FF:11749-123G3: 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 17:18, 29 March 2012


Name:mesenchymal precursor cell - adipose, donor3
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
sexNA
ageNA
cell typemesenchymal precursor cell
cell lineNA
companyNA
collaborationClaudio Schneider LNCIB
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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
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-lymphoma0.0709
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
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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: CNhs12365

Jaspar motifP-value
MA0002.20.655
MA0003.10.36
MA0004.10.757
MA0006.10.967
MA0007.10.36
MA0009.10.125
MA0014.10.659
MA0017.10.795
MA0018.21.01248e-5
MA0019.10.841
MA0024.10.0428
MA0025.10.00254
MA0027.10.322
MA0028.10.869
MA0029.10.255
MA0030.10.00259
MA0031.10.0163
MA0035.20.105
MA0038.10.0606
MA0039.20.169
MA0040.10.259
MA0041.10.4
MA0042.10.675
MA0043.10.00809
MA0046.10.0457
MA0047.20.477
MA0048.10.321
MA0050.10.035
MA0051.10.378
MA0052.10.269
MA0055.10.299
MA0057.10.587
MA0058.10.746
MA0059.10.0369
MA0060.19.33417e-7
MA0061.10.976
MA0062.20.0174
MA0065.20.841
MA0066.10.473
MA0067.10.0175
MA0068.10.0627
MA0069.10.226
MA0070.10.386
MA0071.10.566
MA0072.10.56
MA0073.10.904
MA0074.10.554
MA0076.10.937
MA0077.10.273
MA0078.10.747
MA0079.20.0857
MA0080.28.92513e-7
MA0081.10.034
MA0083.10.00905
MA0084.10.452
MA0087.10.804
MA0088.10.13
MA0090.10.101
MA0091.10.0067
MA0092.10.112
MA0093.10.811
MA0099.21.17139e-4
MA0100.10.848
MA0101.10.085
MA0102.20.788
MA0103.10.0015
MA0104.20.345
MA0105.10.0106
MA0106.10.00682
MA0107.10.0217
MA0108.20.863
MA0111.10.98
MA0112.20.00129
MA0113.10.185
MA0114.10.79
MA0115.10.416
MA0116.10.00194
MA0117.10.929
MA0119.10.0125
MA0122.10.477
MA0124.10.29
MA0125.10.245
MA0131.10.75
MA0135.10.0507
MA0136.19.15019e-6
MA0137.20.174
MA0138.20.803
MA0139.10.672
MA0140.10.464
MA0141.10.244
MA0142.10.767
MA0143.10.285
MA0144.10.184
MA0145.10.161
MA0146.10.957
MA0147.10.12
MA0148.10.75
MA0149.10.698
MA0150.10.225
MA0152.10.00112
MA0153.10.982
MA0154.10.0881
MA0155.10.704
MA0156.10.00202
MA0157.10.745
MA0159.10.269
MA0160.10.46
MA0162.10.204
MA0163.11.5394e-6
MA0164.10.764
MA0258.10.293
MA0259.10.266



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: CNhs12365

Novel motifP-value
10.101
100.12
1000.886
1010.988
1020.0192
1030.141
1040.804
1050.225
1060.861
1070.84
1080.653
1090.378
110.143
1100.0204
1110.787
1120.0364
1130.035
1140.0638
1150.714
1160.105
1170.138
1180.806
1190.836
120.781
1200.135
1210.734
1220.0155
1230.00529
1240.407
1250.966
1260.641
1270.849
1280.757
1290.8
130.125
1300.727
1310.401
1320.941
1330.36
1340.419
1350.871
1360.457
1370.93
1380.774
1390.492
140.229
1400.846
1410.529
1420.378
1430.567
1440.625
1450.805
1460.499
1470.0367
1480.516
1490.0262
150.398
1500.563
1510.776
1520.834
1530.45
1540.873
1550.00704
1560.672
1570.855
1580.00691
1590.0865
160.00478
1600.306
1610.758
1620.787
1630.314
1640.0261
1650.622
1660.0609
1670.662
1680.667
1690.00828
170.55
180.0568
190.0334
20.394
200.266
210.187
220.213
230.272
240.705
250.817
260.213
270.267
280.254
290.0612
30.205
300.727
310.888
328.49958e-11
330.581
340.967
350.282
360.451
370.0601
380.889
390.161
40.307
400.572
410.987
420.713
430.207
440.672
450.858
460.122
470.581
480.471
490.787
50.466
500.555
510.482
520.87
530.0966
540.687
550.0748
560.999
570.741
580.728
590.117
60.146
600.733
610.922
620.3
630.319
640.657
650.501
660.721
670.598
680.644
690.532
70.569
700.228
710.00609
720.78
730.504
740.00781
750.139
760.674
770.0304
780.0915
790.0767
80.0101
800.869
810.277
820.308
830.677
840.782
850.229
860.37
870.352
880.489
890.0503
90.248
900.391
910.455
920.117
930.822
940.573
950.13
960.849
970.186
980.807
990.00827



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: CNhs12365


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)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002570 (mesenchymal stem cell of adipose)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001013 (adipose 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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