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FF:11748-123G2: 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, donor2
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-penis0.0116
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-lymphoma-0.0141
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: CNhs12364

Jaspar motifP-value
MA0002.20.4
MA0003.10.578
MA0004.10.826
MA0006.10.902
MA0007.10.752
MA0009.10.149
MA0014.10.515
MA0017.10.36
MA0018.20.107
MA0019.10.388
MA0024.10.00652
MA0025.10.322
MA0027.10.412
MA0028.10.718
MA0029.10.12
MA0030.10.128
MA0031.10.0258
MA0035.20.00958
MA0038.10.534
MA0039.20.018
MA0040.10.349
MA0041.10.599
MA0042.10.901
MA0043.10.836
MA0046.10.0603
MA0047.20.925
MA0048.10.0102
MA0050.10.135
MA0051.10.483
MA0052.10.365
MA0055.10.00783
MA0057.10.85
MA0058.10.662
MA0059.10.201
MA0060.10.0101
MA0061.10.211
MA0062.20.00413
MA0065.20.33
MA0066.10.891
MA0067.10.809
MA0068.10.92
MA0069.10.182
MA0070.10.245
MA0071.10.737
MA0072.10.764
MA0073.10.851
MA0074.10.217
MA0076.10.563
MA0077.10.102
MA0078.10.942
MA0079.20.368
MA0080.22.65693e-8
MA0081.10.0132
MA0083.11.23998e-4
MA0084.10.104
MA0087.10.87
MA0088.10.701
MA0090.10.0123
MA0091.10.131
MA0092.10.493
MA0093.10.57
MA0099.20.0181
MA0100.10.612
MA0101.10.0711
MA0102.20.795
MA0103.11.68282e-4
MA0104.20.971
MA0105.10.583
MA0106.10.145
MA0107.10.0317
MA0108.20.109
MA0111.10.165
MA0112.20.0207
MA0113.10.198
MA0114.10.31
MA0115.10.433
MA0116.10.912
MA0117.10.16
MA0119.10.435
MA0122.10.125
MA0124.10.109
MA0125.10.0371
MA0131.10.669
MA0135.10.384
MA0136.13.18198e-10
MA0137.20.331
MA0138.20.637
MA0139.10.867
MA0140.10.154
MA0141.10.896
MA0142.10.65
MA0143.10.453
MA0144.10.52
MA0145.10.532
MA0146.10.484
MA0147.10.795
MA0148.10.559
MA0149.10.365
MA0150.10.119
MA0152.11.22386e-4
MA0153.10.322
MA0154.10.775
MA0155.10.332
MA0156.18.3243e-6
MA0157.10.0841
MA0159.10.834
MA0160.10.0647
MA0162.10.209
MA0163.10.0369
MA0164.10.97
MA0258.10.592
MA0259.10.734



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: CNhs12364

Novel motifP-value
10.973
100.751
1000.308
1010.51
1020.0958
1030.878
1040.728
1050.189
1060.893
1070.44
1080.683
1090.797
110.714
1100.0799
1110.488
1120.467
1135.05905e-4
1140.839
1150.769
1160.219
1170.194
1180.74
1190.547
120.762
1200.397
1210.946
1220.0194
1231.75085e-4
1240.137
1250.925
1260.666
1270.623
1280.905
1290.534
130.543
1300.488
1310.794
1320.864
1330.132
1340.196
1350.503
1360.737
1370.656
1380.602
1390.72
140.039
1400.548
1410.526
1420.893
1430.613
1440.724
1450.517
1460.635
1470.0909
1480.144
1490.0515
150.629
1500.126
1510.475
1520.0297
1530.411
1540.929
1550.0145
1560.293
1570.974
1580.00907
1590.141
160.113
1600.398
1610.48
1620.511
1630.226
1640.0328
1650.648
1660.298
1670.765
1680.759
1690.0407
170.853
180.03
190.0418
20.92
200.94
210.0367
220.487
230.684
240.254
250.133
260.945
270.724
280.327
290.176
30.986
300.683
310.782
321.96779e-13
330.693
340.964
350.678
360.0232
370.0467
380.27
390.521
40.492
400.0354
410.0509
420.284
430.788
440.683
450.4
460.681
470.585
480.98
490.121
50.912
500.608
510.951
520.911
530.036
540.909
550.448
560.447
570.424
580.349
590.866
60.478
600.937
610.644
620.648
630.69
640.838
650.833
660.615
670.758
680.493
690.531
70.271
700.673
710.425
720.48
730.0205
740.042
750.136
760.69
770.264
780.0865
790.0668
80.632
800.724
810.728
820.843
830.699
840.87
850.6
860.215
870.362
880.667
890.309
90.688
900.944
910.351
920.748
930.978
940.633
950.0565
960.482
970.317
980.1
990.358



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: CNhs12364


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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