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FF:11537-120A7: 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 16:46, 29 March 2012


Name:Mesenchymal Stem Cells - 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 stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC7515
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-0.0887
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11345

Jaspar motifP-value
MA0002.20.176
MA0003.10.174
MA0004.10.347
MA0006.10.2
MA0007.10.00939
MA0009.10.751
MA0014.10.95
MA0017.10.27
MA0018.20.216
MA0019.10.0971
MA0024.15.62491e-5
MA0025.10.533
MA0027.10.279
MA0028.10.0169
MA0029.10.237
MA0030.10.718
MA0031.10.837
MA0035.20.379
MA0038.10.782
MA0039.20.229
MA0040.10.47
MA0041.10.169
MA0042.10.453
MA0043.10.256
MA0046.10.241
MA0047.20.937
MA0048.10.817
MA0050.10.171
MA0051.10.637
MA0052.10.206
MA0055.10.336
MA0057.10.37
MA0058.10.192
MA0059.10.594
MA0060.10.686
MA0061.10.943
MA0062.22.06641e-4
MA0065.20.052
MA0066.10.398
MA0067.10.106
MA0068.10.769
MA0069.10.301
MA0070.10.0404
MA0071.10.162
MA0072.10.609
MA0073.10.966
MA0074.10.154
MA0076.10.0019
MA0077.10.225
MA0078.10.731
MA0079.20.279
MA0080.20.00615
MA0081.10.256
MA0083.12.68721e-5
MA0084.10.422
MA0087.10.755
MA0088.10.287
MA0090.10.0244
MA0091.10.0125
MA0092.10.655
MA0093.10.359
MA0099.20.305
MA0100.10.0765
MA0101.10.536
MA0102.20.464
MA0103.10.362
MA0104.20.512
MA0105.10.973
MA0106.10.99
MA0107.10.817
MA0108.28.16602e-7
MA0111.10.175
MA0112.20.00403
MA0113.10.00848
MA0114.10.213
MA0115.10.833
MA0116.10.277
MA0117.10.339
MA0119.10.775
MA0122.10.829
MA0124.10.53
MA0125.10.83
MA0131.10.356
MA0135.10.21
MA0136.11.15145e-4
MA0137.20.855
MA0138.20.114
MA0139.10.995
MA0140.10.938
MA0141.10.033
MA0142.10.718
MA0143.10.468
MA0144.10.782
MA0145.10.232
MA0146.10.0128
MA0147.10.441
MA0148.10.837
MA0149.10.952
MA0150.10.807
MA0152.10.469
MA0153.10.138
MA0154.10.146
MA0155.10.0595
MA0156.11.2346e-4
MA0157.10.794
MA0159.10.606
MA0160.10.0565
MA0162.10.168
MA0163.10.237
MA0164.10.978
MA0258.10.0229
MA0259.10.347



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: CNhs11345

Novel motifP-value
10.693
100.467
1000.869
1010.308
1020.788
1030.497
1040.407
1050.135
1060.0642
1070.0653
1080.785
1090.29
110.198
1100.495
1110.801
1120.954
1130.232
1140.792
1150.496
1160.196
1170.777
1180.679
1190.51
120.443
1200.639
1210.314
1220.853
1230.0033
1240.62
1250.226
1260.477
1270.722
1280.0319
1290.266
130.949
1300.0363
1310.653
1320.231
1330.806
1340.52
1350.714
1360.866
1370.0153
1380.198
1390.94
140.628
1400.0858
1410.224
1420.477
1430.587
1440.292
1450.364
1460.218
1470.139
1480.455
1490.0141
150.498
1500.277
1510.575
1520.0712
1530.86
1540.133
1550.666
1560.786
1570.0179
1580.209
1590.773
160.117
1600.0842
1610.354
1620.0718
1630.846
1640.553
1650.0484
1660.642
1670.0178
1680.714
1690.0534
170.268
180.478
190.122
20.107
200.366
210.425
220.0553
230.355
240.814
250.3
260.18
270.28
280.0654
290.775
30.984
300.0775
310.224
321.33862e-6
330.861
340.0956
350.587
360.304
370.258
380.503
390.464
40.773
400.304
410.27
420.593
430.322
440.854
450.244
460.246
470.62
480.283
490.519
50.571
500.209
510.424
520.251
530.768
540.513
550.283
560.462
570.635
580.655
590.0455
60.351
600.375
610.608
620.629
630.425
640.382
650.0483
660.803
670.57
680.0153
690.197
70.768
700.212
710.279
720.488
730.0433
740.448
750.913
760.371
770.0241
780.562
790.593
80.211
800.73
810.442
820.695
830.483
840.447
850.132
860.86
870.0505
880.467
890.275
90.0757
900.0476
910.605
920.695
930.953
940.37
950.295
960.396
970.457
980.344
990.0447



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: CNhs11345


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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