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FF:11217-116B2: 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 16:33, 29 March 2012


Name:Mesenchymal stem cells - adipose, donor0
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
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number7515
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-0.143
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-lymphoma0.459
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs10844

Jaspar motifP-value
MA0002.20.78
MA0003.10.256
MA0004.10.4
MA0006.10.782
MA0007.10.00762
MA0009.10.899
MA0014.10.782
MA0017.10.317
MA0018.24.29253e-4
MA0019.10.778
MA0024.10.00229
MA0025.10.111
MA0027.10.83
MA0028.10.238
MA0029.10.77
MA0030.18.32454e-4
MA0031.10.132
MA0035.20.486
MA0038.10.176
MA0039.20.887
MA0040.10.532
MA0041.10.62
MA0042.10.661
MA0043.12.09746e-4
MA0046.10.37
MA0047.20.477
MA0048.10.104
MA0050.10.0204
MA0051.10.461
MA0052.10.7
MA0055.10.0184
MA0057.10.489
MA0058.10.446
MA0059.10.00329
MA0060.10.959
MA0061.10.427
MA0062.20.403
MA0065.20.102
MA0066.10.144
MA0067.10.0712
MA0068.10.104
MA0069.10.913
MA0070.10.19
MA0071.10.115
MA0072.10.769
MA0073.10.865
MA0074.10.462
MA0076.10.788
MA0077.10.425
MA0078.10.872
MA0079.20.0797
MA0080.20.0279
MA0081.10.259
MA0083.10.0757
MA0084.10.00133
MA0087.10.385
MA0088.10.00345
MA0090.10.0442
MA0091.10.0427
MA0092.10.128
MA0093.10.362
MA0099.23.20241e-6
MA0100.10.362
MA0101.10.924
MA0102.20.00675
MA0103.10.0066
MA0104.20.0876
MA0105.10.00796
MA0106.10.0221
MA0107.10.769
MA0108.20.0145
MA0111.10.708
MA0112.25.56952e-5
MA0113.10.0595
MA0114.10.283
MA0115.10.93
MA0116.10.00669
MA0117.10.538
MA0119.10.0324
MA0122.10.712
MA0124.10.521
MA0125.10.617
MA0131.10.646
MA0135.10.172
MA0136.10.322
MA0137.20.944
MA0138.20.223
MA0139.10.885
MA0140.10.624
MA0141.10.00692
MA0142.10.819
MA0143.10.859
MA0144.10.363
MA0145.10.379
MA0146.10.693
MA0147.10.0226
MA0148.10.566
MA0149.10.0491
MA0150.10.0963
MA0152.10.0112
MA0153.10.919
MA0154.10.0548
MA0155.10.94
MA0156.10.869
MA0157.10.601
MA0159.10.465
MA0160.10.325
MA0162.10.207
MA0163.16.88709e-6
MA0164.10.839
MA0258.10.0739
MA0259.10.211



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: CNhs10844

Novel motifP-value
10.0105
100.1
1000.201
1010.549
1020.901
1030.202
1040.323
1050.955
1060.381
1070.0396
1080.936
1090.0136
110.0412
1100.0117
1110.355
1120.664
1130.0734
1140.383
1150.92
1160.0774
1170.135
1180.98
1190.283
120.85
1200.294
1210.304
1220.779
1230.476
1240.695
1250.0872
1260.912
1270.886
1280.486
1290.716
130.0646
1300.00456
1310.874
1320.675
1330.548
1340.0441
1350.916
1360.912
1370.632
1380.46
1390.887
140.159
1400.821
1410.185
1420.438
1430.0452
1440.688
1450.177
1460.1
1470.0523
1480.0452
1490.29
150.0907
1500.164
1510.75
1520.263
1530.817
1540.911
1550.0589
1560.919
1570.618
1580.123
1590.135
160.035
1600.0879
1610.952
1620.38
1630.974
1640.567
1650.657
1660.522
1670.822
1680.115
1690.00709
170.181
180.0673
190.041
20.685
200.551
210.0475
220.391
230.597
240.172
250.704
260.0676
270.647
280.241
290.0734
30.09
300.831
310.838
322.47849e-5
330.0847
340.451
350.764
360.0361
370.0553
380.44
390.191
40.583
400.15
410.722
420.236
430.168
440.587
450.979
460.0328
470.0915
480.0924
490.287
50.288
500.263
510.314
520.83
530.894
540.814
550.717
560.716
570.203
580.967
590.204
60.623
600.604
610.457
620.455
630.188
640.493
650.269
660.197
670.386
680.927
690.523
70.352
700.887
710.0195
720.499
730.0711
740.0531
750.119
760.684
770.0959
780.521
790.347
80.00284
800.735
810.381
820.968
830.04
840.992
850.795
860.869
870.0379
880.783
890.0368
90.247
900.105
910.59
920.281
930.619
940.0693
950.0819
960.244
970.274
980.513
990.0177



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: CNhs10844


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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