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FF:11214-116A8: 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 17:20, 29 March 2012


Name:Mesenchymal stem cells - umbilical, donor0
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
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 number7535
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-0.0968
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-lymphoma0.412
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12492

Jaspar motifP-value
MA0002.20.789
MA0003.10.414
MA0004.10.731
MA0006.10.737
MA0007.10.0524
MA0009.10.815
MA0014.10.918
MA0017.10.0211
MA0018.20.0019
MA0019.10.293
MA0024.10.0342
MA0025.10.00234
MA0027.10.479
MA0028.10.0951
MA0029.10.746
MA0030.10.00181
MA0031.10.0232
MA0035.20.315
MA0038.10.0381
MA0039.20.883
MA0040.10.528
MA0041.10.951
MA0042.10.569
MA0043.10.00858
MA0046.10.764
MA0047.20.983
MA0048.10.147
MA0050.17.91765e-8
MA0051.12.79958e-5
MA0052.10.14
MA0055.17.99598e-4
MA0057.10.371
MA0058.10.822
MA0059.10.0045
MA0060.10.00549
MA0061.10.549
MA0062.20.787
MA0065.20.0169
MA0066.10.0595
MA0067.10.0237
MA0068.10.269
MA0069.10.669
MA0070.10.35
MA0071.10.0581
MA0072.10.961
MA0073.10.769
MA0074.10.192
MA0076.10.509
MA0077.10.287
MA0078.10.634
MA0079.20.142
MA0080.23.94887e-7
MA0081.10.0995
MA0083.10.00991
MA0084.10.109
MA0087.10.944
MA0088.10.0135
MA0090.10.155
MA0091.10.068
MA0092.10.176
MA0093.10.784
MA0099.20.298
MA0100.10.172
MA0101.10.874
MA0102.20.115
MA0103.10.638
MA0104.20.136
MA0105.10.00922
MA0106.10.0401
MA0107.10.562
MA0108.20.00468
MA0111.10.41
MA0112.20.00132
MA0113.10.0441
MA0114.10.0287
MA0115.10.197
MA0116.10.009
MA0117.10.774
MA0119.10.0284
MA0122.10.739
MA0124.10.89
MA0125.10.83
MA0131.10.712
MA0135.10.127
MA0136.18.68068e-4
MA0137.20.895
MA0138.20.171
MA0139.10.426
MA0140.10.0963
MA0141.10.0248
MA0142.10.788
MA0143.10.875
MA0144.10.825
MA0145.10.319
MA0146.10.109
MA0147.10.0655
MA0148.10.575
MA0149.10.239
MA0150.10.829
MA0152.10.59
MA0153.10.557
MA0154.10.0869
MA0155.10.469
MA0156.10.255
MA0157.10.115
MA0159.10.268
MA0160.10.285
MA0162.10.0706
MA0163.12.75043e-7
MA0164.10.447
MA0258.10.0205
MA0259.10.25



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: CNhs12492

Novel motifP-value
10.0242
100.12
1000.127
1010.609
1020.693
1030.0626
1040.0553
1050.808
1060.603
1070.233
1080.924
1090.0112
110.0231
1100.0207
1110.602
1120.844
1130.751
1140.253
1150.743
1160.0139
1170.168
1180.13
1190.429
120.538
1200.037
1210.805
1220.448
1230.417
1240.94
1250.403
1260.416
1270.0747
1280.405
1290.842
130.0543
1300.0596
1310.385
1320.654
1330.335
1340.886
1350.729
1360.231
1370.133
1380.0729
1390.811
140.653
1400.795
1410.809
1420.466
1430.185
1440.754
1450.497
1460.0689
1470.232
1480.11
1490.199
150.23
1500.583
1510.623
1520.43
1530.334
1540.667
1550.352
1560.54
1570.859
1580.193
1590.425
160.0503
1600.0202
1610.329
1620.355
1630.687
1640.255
1650.756
1660.626
1670.226
1680.514
1690.0335
170.242
180.288
190.144
20.778
200.986
210.64
220.293
230.947
240.0902
250.635
260.0129
270.525
280.322
290.0899
30.0701
300.902
310.582
327.59088e-6
330.0838
340.701
350.581
360.0644
370.0435
380.285
390.313
40.818
400.015
410.265
420.259
430.194
440.165
450.91
460.0513
470.042
480.0401
490.256
50.819
500.351
510.177
520.518
530.509
540.858
550.93
560.558
570.179
580.879
590.0817
60.751
600.973
610.234
620.371
630.139
640.0511
650.158
660.133
670.325
680.865
690.286
70.396
700.344
710.0121
720.628
730.202
740.465
750.212
760.663
770.102
780.66
790.042
80.0116
800.94
810.363
820.384
830.0643
840.275
850.536
860.898
870.244
880.52
890.0254
90.504
900.705
910.992
920.983
930.591
940.116
950.0647
960.597
970.834
980.436
990.001



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: CNhs12492


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)
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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