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FF:11549-120C1: 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:Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueumbilical cord
dev stagefetus
sexfemale
age?
cell typemesenchymal stem cell
cell lineNA
companyCET
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.0722
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-0.0634
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11350

Jaspar motifP-value
MA0002.20.467
MA0003.10.936
MA0004.10.788
MA0006.10.143
MA0007.10.594
MA0009.10.0458
MA0014.10.507
MA0017.10.181
MA0018.29.64296e-6
MA0019.10.242
MA0024.10.00831
MA0025.10.0017
MA0027.10.509
MA0028.10.734
MA0029.10.185
MA0030.10.167
MA0031.10.0263
MA0035.20.234
MA0038.10.39
MA0039.20.517
MA0040.10.563
MA0041.10.374
MA0042.10.628
MA0043.10.00309
MA0046.10.709
MA0047.20.42
MA0048.10.14
MA0050.13.61559e-5
MA0051.10.033
MA0052.10.205
MA0055.10.174
MA0057.10.149
MA0058.10.897
MA0059.10.621
MA0060.12.93026e-4
MA0061.10.0943
MA0062.20.00603
MA0065.20.154
MA0066.10.477
MA0067.10.0184
MA0068.10.0421
MA0069.10.238
MA0070.10.499
MA0071.10.655
MA0072.10.811
MA0073.10.572
MA0074.10.903
MA0076.10.287
MA0077.10.992
MA0078.10.692
MA0079.20.914
MA0080.27.5718e-9
MA0081.10.0192
MA0083.10.00197
MA0084.10.123
MA0087.10.904
MA0088.10.392
MA0090.12.00869e-5
MA0091.10.414
MA0092.10.409
MA0093.10.967
MA0099.20.266
MA0100.10.563
MA0101.10.00751
MA0102.25.62093e-4
MA0103.10.0148
MA0104.20.0286
MA0105.10.678
MA0106.10.296
MA0107.10.0167
MA0108.20.414
MA0111.10.0607
MA0112.20.0484
MA0113.10.602
MA0114.10.0408
MA0115.10.047
MA0116.10.643
MA0117.10.358
MA0119.10.229
MA0122.10.399
MA0124.10.995
MA0125.10.732
MA0131.10.677
MA0135.10.435
MA0136.16.71596e-9
MA0137.20.044
MA0138.20.607
MA0139.10.541
MA0140.10.72
MA0141.10.45
MA0142.10.14
MA0143.10.565
MA0144.10.388
MA0145.10.707
MA0146.10.772
MA0147.10.192
MA0148.10.624
MA0149.10.726
MA0150.10.448
MA0152.10.0619
MA0153.10.563
MA0154.10.408
MA0155.10.858
MA0156.12.58901e-7
MA0157.10.124
MA0159.10.491
MA0160.10.0311
MA0162.10.0194
MA0163.10.332
MA0164.10.837
MA0258.10.575
MA0259.10.728



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: CNhs11350

Novel motifP-value
10.653
100.438
1000.661
1010.528
1020.261
1030.372
1040.895
1050.55
1060.549
1070.317
1080.796
1090.473
110.761
1100.946
1110.675
1120.448
1138.90759e-4
1140.343
1150.397
1160.412
1170.787
1180.719
1190.865
120.133
1200.204
1210.317
1220.333
1234.06178e-5
1240.136
1250.672
1260.511
1270.559
1280.432
1290.612
130.551
1300.237
1310.749
1320.523
1330.25
1340.161
1350.799
1360.692
1370.572
1380.262
1390.584
140.113
1400.949
1410.212
1420.342
1430.844
1440.748
1450.491
1460.863
1470.254
1480.436
1490.0141
150.752
1500.957
1510.719
1520.1
1530.536
1540.741
1550.0188
1560.667
1570.0641
1580.0155
1590.531
160.0212
1600.863
1610.434
1620.892
1630.766
1640.411
1650.629
1660.0525
1670.612
1680.304
1690.0323
170.962
180.0576
190.0435
20.666
200.882
210.0319
220.214
230.258
240.484
250.524
260.927
270.73
280.342
290.332
30.689
300.509
310.362
323.49966e-15
330.339
340.615
350.0613
360.0895
370.07
380.236
390.676
40.638
400.79
410.906
420.776
430.739
440.335
450.693
460.806
470.855
480.873
490.768
50.711
500.751
510.254
520.399
530.0295
540.932
550.277
560.821
570.614
580.191
590.0733
60.429
600.254
610.436
620.996
630.869
640.469
650.967
660.928
670.144
680.724
690.305
70.687
700.529
710.22
720.363
730.0308
740.536
750.172
760.583
770.0727
780.889
790.0605
80.325
800.975
810.907
820.8
830.602
840.0896
850.371
860.977
870.0722
880.514
890.0972
90.981
900.129
910.738
920.37
930.68
940.875
950.619
960.792
970.37
980.152
990.142



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: CNhs11350


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)
0000081 (blood cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0000988 (hematopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002569 (mesenchymal stem cell of umbilical cord)

UBERON: Anatomy
0000061 (anatomical structure)
0000087 (inner cell mass)
0000091 (bilaminar disc)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000479 (tissue)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002331 (umbilical cord)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003422 (mesenchyme of umbilical cord)
0004120 (mesoderm-derived structure)
0005423 (developing anatomical structure)
0005728 (extraembryonic mesoderm)
0007806 (connecting stalk)
0008780 (inner cell mass derived epiblast)
0009142 (entire embryonic mesenchyme)

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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