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FF:11840-124H4: 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 17:29, 29 March 2012


Name:mesenchymal precursor cell - bone marrow, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
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 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
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-0.287
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: CNhs13098

Jaspar motifP-value
MA0002.20.721
MA0003.10.381
MA0004.10.743
MA0006.10.436
MA0007.10.548
MA0009.10.551
MA0014.10.814
MA0017.10.547
MA0018.26.52201e-5
MA0019.10.5
MA0024.15.47011e-6
MA0025.13.2064e-6
MA0027.10.776
MA0028.10.0369
MA0029.10.898
MA0030.10.0074
MA0031.10.163
MA0035.23.42295e-4
MA0038.18.92335e-4
MA0039.20.0924
MA0040.10.966
MA0041.10.165
MA0042.10.185
MA0043.16.16037e-4
MA0046.10.211
MA0047.20.766
MA0048.10.847
MA0050.12.5588e-7
MA0051.15.44033e-7
MA0052.10.276
MA0055.10.097
MA0057.10.256
MA0058.10.846
MA0059.10.72
MA0060.12.75186e-15
MA0061.10.967
MA0062.23.1207e-9
MA0065.20.289
MA0066.10.42
MA0067.10.0828
MA0068.10.628
MA0069.10.211
MA0070.10.594
MA0071.10.768
MA0072.10.637
MA0073.10.678
MA0074.10.0879
MA0076.10.00504
MA0077.10.194
MA0078.10.622
MA0079.20.218
MA0080.25.73155e-9
MA0081.10.0149
MA0083.11.02725e-4
MA0084.10.595
MA0087.10.665
MA0088.10.496
MA0090.10.00821
MA0091.16.34861e-4
MA0092.10.317
MA0093.10.818
MA0099.20.0712
MA0100.10.243
MA0101.10.0553
MA0102.20.552
MA0103.10.00473
MA0104.20.478
MA0105.10.0354
MA0106.10.015
MA0107.10.0382
MA0108.20.104
MA0111.10.499
MA0112.26.02815e-4
MA0113.10.187
MA0114.10.481
MA0115.10.606
MA0116.10.00632
MA0117.10.479
MA0119.10.0869
MA0122.10.994
MA0124.10.739
MA0125.10.453
MA0131.10.446
MA0135.10.7
MA0136.11.3593e-8
MA0137.20.0801
MA0138.20.93
MA0139.10.33
MA0140.10.0389
MA0141.10.0688
MA0142.10.113
MA0143.10.0323
MA0144.10.123
MA0145.10.141
MA0146.10.77
MA0147.10.644
MA0148.10.207
MA0149.10.135
MA0150.10.665
MA0152.10.00859
MA0153.10.111
MA0154.10.169
MA0155.10.561
MA0156.13.36793e-9
MA0157.10.843
MA0159.10.36
MA0160.10.945
MA0162.10.173
MA0163.11.75249e-4
MA0164.10.35
MA0258.10.244
MA0259.10.842



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: CNhs13098

Novel motifP-value
10.328
100.281
1000.564
1010.792
1020.0404
1030.0178
1040.685
1050.0688
1060.279
1070.104
1080.283
1090.626
110.386
1100.319
1110.7
1120.306
1130.137
1140.0111
1150.201
1160.138
1170.933
1180.668
1190.327
120.575
1200.187
1210.629
1220.0115
1230.17
1240.49
1250.782
1260.777
1270.648
1280.485
1290.566
130.736
1300.182
1310.419
1320.296
1330.678
1340.203
1350.966
1360.734
1370.887
1380.67
1390.578
140.507
1400.341
1410.221
1420.301
1430.745
1440.181
1450.329
1460.827
1470.116
1480.331
1490.16
150.605
1500.432
1510.487
1520.132
1530.148
1540.846
1550.0715
1560.0568
1570.763
1580.00636
1590.229
160.0214
1600.329
1610.797
1620.423
1630.648
1640.072
1650.502
1660.00537
1670.526
1680.118
1690.014
170.382
180.0948
190.00768
20.332
200.237
210.0463
220.149
230.0324
240.908
250.652
260.847
270.402
280.303
290.113
30.126
300.831
310.446
325.57233e-9
330.546
340.687
350.439
360.14
370.0349
380.81
390.0363
40.0191
400.23
410.321
420.817
430.173
440.613
450.772
460.134
470.915
480.942
490.683
50.491
500.395
510.69
520.49
530.402
540.983
550.193
560.652
570.975
580.7
590.0384
60.0268
600.371
610.633
620.318
630.0525
640.866
650.195
660.0863
670.279
680.771
690.488
70.563
700.0119
710.0741
720.454
730.065
740.209
750.373
760.764
770.0373
780.224
794.70574e-4
80.0566
800.373
810.5
820.095
830.804
840.348
850.259
860.35
870.418
880.362
890.00999
90.15
900.29
910.55
920.036
930.583
940.566
950.928
960.847
970.507
980.938
990.015



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: CNhs13098


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)
0002092 (bone marrow cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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