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FF:11629-122B9: 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 17:11, 29 March 2012


Name:Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor2
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 stageNA
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-0.08
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-0.338
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: CNhs12105

Jaspar motifP-value
MA0002.20.677
MA0003.10.361
MA0004.10.64
MA0006.10.39
MA0007.10.858
MA0009.10.36
MA0014.10.243
MA0017.10.633
MA0018.23.47351e-5
MA0019.10.692
MA0024.14.29234e-5
MA0025.10.00168
MA0027.10.479
MA0028.10.00177
MA0029.10.0756
MA0030.10.399
MA0031.10.271
MA0035.20.73
MA0038.10.178
MA0039.20.733
MA0040.10.804
MA0041.10.253
MA0042.10.293
MA0043.10.00108
MA0046.10.899
MA0047.20.976
MA0048.10.656
MA0050.16.26128e-4
MA0051.10.00572
MA0052.10.206
MA0055.10.335
MA0057.10.234
MA0058.10.602
MA0059.10.771
MA0060.19.44966e-7
MA0061.10.683
MA0062.28.40457e-9
MA0065.20.869
MA0066.10.289
MA0067.10.023
MA0068.10.169
MA0069.10.475
MA0070.10.929
MA0071.10.884
MA0072.10.302
MA0073.10.967
MA0074.10.217
MA0076.13.06e-4
MA0077.10.74
MA0078.10.707
MA0079.20.906
MA0080.25.15568e-11
MA0081.16.83024e-4
MA0083.10.0845
MA0084.10.678
MA0087.10.786
MA0088.10.534
MA0090.13.15506e-4
MA0091.10.0731
MA0092.10.454
MA0093.10.58
MA0099.20.00255
MA0100.10.102
MA0101.10.0506
MA0102.20.00444
MA0103.10.53
MA0104.20.212
MA0105.10.4
MA0106.10.104
MA0107.10.044
MA0108.20.0302
MA0111.10.686
MA0112.20.00148
MA0113.10.135
MA0114.10.676
MA0115.10.00489
MA0116.10.107
MA0117.10.401
MA0119.10.126
MA0122.11
MA0124.10.0283
MA0125.10.0251
MA0131.10.173
MA0135.10.948
MA0136.11.70896e-13
MA0137.20.185
MA0138.20.102
MA0139.10.208
MA0140.10.899
MA0141.10.556
MA0142.10.576
MA0143.10.587
MA0144.10.584
MA0145.10.901
MA0146.10.196
MA0147.10.198
MA0148.10.5
MA0149.10.774
MA0150.10.0946
MA0152.10.0738
MA0153.10.172
MA0154.10.0528
MA0155.10.107
MA0156.11.72519e-13
MA0157.10.541
MA0159.10.138
MA0160.10.425
MA0162.10.0389
MA0163.10.0455
MA0164.10.651
MA0258.10.0376
MA0259.10.367



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: CNhs12105

Novel motifP-value
10.588
100.644
1000.793
1010.459
1020.112
1030.309
1040.923
1050.889
1060.361
1070.164
1080.413
1090.597
110.127
1100.351
1110.414
1120.596
1130.00654
1140.202
1150.268
1160.316
1170.935
1180.868
1190.505
120.196
1200.394
1210.73
1220.363
1230.00906
1240.736
1250.691
1260.812
1270.524
1280.499
1290.747
130.864
1300.294
1310.345
1320.142
1330.683
1340.129
1350.824
1360.773
1370.399
1380.285
1390.038
140.955
1400.235
1410.729
1420.589
1430.988
1440.46
1450.978
1460.955
1470.68
1480.958
1490.0062
150.907
1500.98
1510.816
1520.272
1530.277
1540.565
1550.502
1560.535
1570.912
1580.0586
1590.526
160.0084
1600.222
1610.0988
1620.883
1630.636
1640.249
1650.734
1660.0423
1670.901
1680.173
1690.00848
170.535
180.0379
190.0824
20.527
200.875
210.177
220.0373
230.0133
240.273
250.808
260.382
270.18
280.439
290.177
30.446
300.142
310.12
321.77983e-18
330.912
340.786
350.739
360.236
370.117
380.955
390.574
40.789
400.983
410.545
420.648
430.195
440.198
450.54
460.151
470.599
480.4
490.471
50.396
500.986
510.828
520.474
530.143
540.159
550.233
560.771
570.244
580.817
590.00775
60.956
600.823
610.988
620.282
630.452
640.503
650.0624
660.72
670.334
680.274
690.276
70.875
700.0422
710.228
720.785
730.502
740.367
750.262
760.468
770.0328
780.696
790.0155
80.0939
800.969
810.597
820.0786
830.0393
840.46
850.156
860.817
870.347
880.254
890.161
90.769
900.297
910.0336
920.068
930.153
940.45
950.905
960.397
970.371
980.802
990.326



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: CNhs12105


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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