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FF:11747-123G1: 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, 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
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-lymphoma0.168
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12363

Jaspar motifP-value
MA0002.20.714
MA0003.10.578
MA0004.10.566
MA0006.10.81
MA0007.10.894
MA0009.10.207
MA0014.10.418
MA0017.10.782
MA0018.25.51235e-4
MA0019.10.66
MA0024.10.971
MA0025.10.0315
MA0027.10.978
MA0028.10.155
MA0029.10.375
MA0030.19.97074e-4
MA0031.10.00808
MA0035.20.033
MA0038.10.175
MA0039.20.102
MA0040.10.945
MA0041.10.733
MA0042.10.985
MA0043.10.00277
MA0046.10.297
MA0047.20.605
MA0048.10.0238
MA0050.14.47979e-4
MA0051.10.0481
MA0052.10.0561
MA0055.10.026
MA0057.10.72
MA0058.10.5
MA0059.10.071
MA0060.10.00383
MA0061.10.626
MA0062.20.219
MA0065.20.552
MA0066.10.749
MA0067.10.0293
MA0068.10.227
MA0069.10.29
MA0070.10.38
MA0071.10.371
MA0072.10.719
MA0073.10.704
MA0074.10.197
MA0076.10.333
MA0077.10.137
MA0078.10.87
MA0079.20.274
MA0080.26.04825e-8
MA0081.10.0225
MA0083.10.00285
MA0084.10.254
MA0087.10.977
MA0088.10.0604
MA0090.10.086
MA0091.10.0306
MA0092.10.162
MA0093.10.789
MA0099.21.24311e-4
MA0100.10.984
MA0101.10.0319
MA0102.20.106
MA0103.12.49737e-4
MA0104.20.657
MA0105.10.145
MA0106.10.0523
MA0107.10.0143
MA0108.20.965
MA0111.10.452
MA0112.20.00274
MA0113.10.271
MA0114.10.712
MA0115.10.515
MA0116.10.00825
MA0117.10.989
MA0119.10.0539
MA0122.10.39
MA0124.10.21
MA0125.10.156
MA0131.10.879
MA0135.10.27
MA0136.11.00291e-6
MA0137.20.313
MA0138.20.86
MA0139.10.813
MA0140.10.179
MA0141.10.382
MA0142.10.926
MA0143.10.534
MA0144.10.251
MA0145.10.346
MA0146.10.601
MA0147.10.261
MA0148.10.496
MA0149.10.913
MA0150.10.473
MA0152.18.50119e-4
MA0153.10.807
MA0154.10.195
MA0155.10.818
MA0156.10.00113
MA0157.10.106
MA0159.10.917
MA0160.10.355
MA0162.10.279
MA0163.14.47507e-5
MA0164.10.881
MA0258.10.482
MA0259.10.585



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: CNhs12363

Novel motifP-value
10.237
100.0965
1000.973
1010.581
1020.136
1030.112
1040.701
1050.0393
1060.941
1070.38
1080.633
1090.278
110.228
1100.0365
1110.697
1120.225
1130.00153
1140.256
1150.152
1160.0263
1170.0923
1180.735
1190.904
120.614
1200.134
1210.683
1220.0169
1236.25455e-4
1240.396
1250.474
1260.859
1270.928
1280.898
1290.948
130.266
1300.447
1310.542
1320.901
1330.414
1340.226
1350.964
1360.829
1370.757
1380.761
1390.846
140.0715
1400.97
1410.871
1420.79
1430.303
1440.702
1450.732
1460.776
1470.0635
1480.991
1490.267
150.675
1500.258
1510.684
1520.288
1530.777
1540.922
1550.0273
1560.364
1570.604
1580.00144
1590.126
160.0177
1600.463
1610.423
1620.507
1630.973
1640.133
1650.829
1660.511
1670.833
1680.679
1690.00582
170.391
180.0276
190.0106
20.346
200.443
210.0279
220.293
230.88
240.853
250.518
260.186
270.555
280.339
290.126
30.212
300.49
310.757
321.8977e-12
330.886
340.512
350.546
360.0483
370.0768
380.434
390.115
40.486
400.175
410.221
420.612
430.431
440.482
450.689
460.202
470.528
480.342
490.716
50.857
500.646
510.732
520.606
530.0533
540.837
550.492
560.948
570.919
580.431
590.0901
60.214
600.836
610.558
620.719
630.607
640.875
650.704
660.871
670.435
680.32
690.666
70.593
700.784
710.0347
720.918
730.139
740.142
750.076
760.94
770.00632
780.103
790.028
80.0224
800.831
810.396
820.734
830.947
840.822
850.726
860.395
870.109
880.694
890.0878
90.308
900.824
910.621
920.69
930.359
940.401
950.0903
960.964
970.654
980.18
990.00607



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: CNhs12363


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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