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FF:11698-123A6: 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 17:27, 29 March 2012


Name:Mesenchymal Stem Cells - 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 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 number2534
catalog numberSC7515
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-penis0.161
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-lymphoma0.377
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: CNhs12922

Jaspar motifP-value
MA0002.20.656
MA0003.10.237
MA0004.10.673
MA0006.10.524
MA0007.10.0143
MA0009.10.675
MA0014.10.861
MA0017.10.103
MA0018.21.9566e-4
MA0019.10.527
MA0024.10.736
MA0025.10.00166
MA0027.10.364
MA0028.10.41
MA0029.10.999
MA0030.11.22174e-4
MA0031.10.0439
MA0035.20.489
MA0038.10.588
MA0039.20.349
MA0040.10.443
MA0041.10.813
MA0042.10.764
MA0043.14.87078e-8
MA0046.10.272
MA0047.20.603
MA0048.10.195
MA0050.10.00173
MA0051.10.0172
MA0052.10.734
MA0055.10.155
MA0057.10.534
MA0058.10.766
MA0059.10.0358
MA0060.10.0242
MA0061.10.603
MA0062.20.00428
MA0065.20.0322
MA0066.10.015
MA0067.10.0122
MA0068.10.006
MA0069.10.522
MA0070.10.666
MA0071.10.141
MA0072.10.269
MA0073.10.835
MA0074.10.143
MA0076.10.0258
MA0077.10.976
MA0078.10.536
MA0079.20.0399
MA0080.25.41638e-5
MA0081.10.0179
MA0083.10.137
MA0084.10.0291
MA0087.10.747
MA0088.10.0204
MA0090.10.277
MA0091.10.0936
MA0092.10.246
MA0093.10.708
MA0099.20.0677
MA0100.10.835
MA0101.10.433
MA0102.20.00637
MA0103.10.412
MA0104.20.29
MA0105.10.0048
MA0106.10.0479
MA0107.10.237
MA0108.20.206
MA0111.10.534
MA0112.21.01561e-5
MA0113.10.207
MA0114.10.177
MA0115.10.574
MA0116.14.78389e-4
MA0117.10.498
MA0119.10.0147
MA0122.10.308
MA0124.10.738
MA0125.10.237
MA0131.10.348
MA0135.10.174
MA0136.11.29982e-4
MA0137.20.164
MA0138.20.175
MA0139.10.992
MA0140.10.979
MA0141.10.0057
MA0142.10.874
MA0143.10.889
MA0144.10.878
MA0145.10.28
MA0146.10.357
MA0147.10.12
MA0148.10.463
MA0149.10.035
MA0150.10.534
MA0152.10.0667
MA0153.10.756
MA0154.10.0272
MA0155.10.745
MA0156.10.0013
MA0157.10.57
MA0159.10.314
MA0160.10.544
MA0162.10.115
MA0163.19.6243e-7
MA0164.10.701
MA0258.10.00603
MA0259.10.635



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: CNhs12922

Novel motifP-value
10.0214
100.0663
1000.153
1010.891
1020.908
1030.107
1040.456
1050.0975
1060.0723
1070.029
1080.313
1090.0482
110.0528
1100.0527
1110.0635
1120.132
1130.136
1140.0986
1150.0872
1160.0489
1170.139
1180.46
1190.238
120.406
1200.0757
1210.999
1220.192
1230.872
1240.696
1250.0473
1260.641
1270.104
1280.14
1290.905
130.0939
1300.329
1310.833
1320.607
1330.471
1340.551
1350.961
1360.744
1370.264
1380.886
1390.473
140.391
1400.145
1410.259
1420.794
1430.0782
1440.688
1450.0765
1460.708
1470.0664
1480.041
1490.399
150.186
1500.174
1510.505
1520.21
1530.955
1540.918
1550.669
1560.561
1570.21
1580.345
1590.272
160.028
1600.0253
1610.883
1620.281
1630.751
1640.249
1650.601
1660.166
1670.174
1680.297
1690.00401
170.186
180.068
190.0433
20.649
200.675
210.061
220.281
230.417
240.41
250.989
260.0186
270.428
280.293
290.0881
30.0761
300.856
310.725
321.95583e-7
330.211
340.629
350.271
360.0619
370.047
380.338
390.266
40.861
400.197
410.589
420.365
430.124
440.0167
450.93
460.0328
470.094
480.105
490.205
50.481
500.683
510.472
520.903
530.555
540.768
550.761
560.59
570.11
580.683
590.0714
60.499
600.47
610.676
620.274
630.12
640.293
650.146
660.89
670.318
680.586
690.164
70.641
700.124
710.0226
720.827
730.076
740.101
750.127
760.726
770.0621
780.536
790.0202
80.00295
800.303
810.253
820.466
830.569
840.389
850.132
860.768
870.148
880.584
890.154
90.381
900.286
910.562
920.15
930.71
940.0521
950.107
960.19
970.462
980.149
990.0164



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: CNhs12922


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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