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FF:11700-123A8: 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 17:12, 29 March 2012


Name:Mesenchymal Stem Cells - umbilical, donor3
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/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC7535
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-lymphoma0.0617
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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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: CNhs12127

Jaspar motifP-value
MA0002.20.5
MA0003.10.179
MA0004.10.853
MA0006.10.309
MA0007.10.0302
MA0009.10.486
MA0014.10.918
MA0017.10.0598
MA0018.20.00107
MA0019.10.766
MA0024.10.243
MA0025.10.0414
MA0027.10.85
MA0028.10.953
MA0029.10.487
MA0030.10.0319
MA0031.19.3509e-5
MA0035.20.0554
MA0038.10.0069
MA0039.20.72
MA0040.10.854
MA0041.10.593
MA0042.10.994
MA0043.10.00227
MA0046.10.154
MA0047.20.192
MA0048.10.331
MA0050.14.72037e-7
MA0051.12.07794e-5
MA0052.10.68
MA0055.10.0374
MA0057.10.285
MA0058.10.883
MA0059.10.203
MA0060.11.45979e-4
MA0061.10.447
MA0062.20.109
MA0065.20.0336
MA0066.10.302
MA0067.10.0152
MA0068.10.393
MA0069.10.478
MA0070.10.149
MA0071.10.0143
MA0072.10.705
MA0073.10.715
MA0074.10.203
MA0076.10.289
MA0077.10.482
MA0078.10.732
MA0079.20.587
MA0080.22.67015e-6
MA0081.10.00641
MA0083.10.0853
MA0084.10.524
MA0087.10.882
MA0088.10.141
MA0090.10.0271
MA0091.10.00663
MA0092.10.0648
MA0093.10.906
MA0099.20.148
MA0100.10.666
MA0101.10.907
MA0102.20.04
MA0103.10.689
MA0104.20.978
MA0105.10.0677
MA0106.10.018
MA0107.10.863
MA0108.20.115
MA0111.10.658
MA0112.28.37915e-4
MA0113.10.0103
MA0114.10.0484
MA0115.10.994
MA0116.10.0363
MA0117.10.629
MA0119.10.0522
MA0122.10.748
MA0124.10.381
MA0125.10.573
MA0131.10.281
MA0135.10.437
MA0136.14.77891e-6
MA0137.20.285
MA0138.20.0672
MA0139.10.682
MA0140.10.0112
MA0141.10.0651
MA0142.10.587
MA0143.10.958
MA0144.10.822
MA0145.10.159
MA0146.10.023
MA0147.10.791
MA0148.10.719
MA0149.10.662
MA0150.10.832
MA0152.10.961
MA0153.10.17
MA0154.10.0647
MA0155.10.174
MA0156.10.00902
MA0157.10.00579
MA0159.10.399
MA0160.10.104
MA0162.10.0977
MA0163.16.93535e-4
MA0164.10.749
MA0258.10.0177
MA0259.10.827



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: CNhs12127

Novel motifP-value
10.0839
100.398
1000.28
1010.589
1020.647
1030.11
1040.425
1050.246
1060.19
1070.0619
1080.574
1090.0193
110.0331
1100.0671
1110.389
1120.974
1130.793
1140.247
1150.819
1160.0652
1170.233
1180.397
1190.212
120.505
1200.2
1210.809
1220.99
1230.315
1240.535
1250.397
1260.38
1270.0346
1280.188
1290.404
130.215
1300.238
1310.99
1320.366
1330.409
1340.322
1350.572
1360.778
1370.093
1380.235
1390.261
140.94
1400.591
1410.507
1420.107
1430.132
1440.597
1450.442
1460.186
1470.165
1480.506
1490.128
150.461
1500.454
1510.331
1520.142
1530.353
1540.541
1550.284
1560.373
1570.618
1580.401
1590.755
160.11
1600.0201
1610.17
1620.0993
1630.509
1640.632
1650.446
1660.388
1670.925
1680.68
1690.0299
170.0584
180.177
190.0926
20.413
200.67
210.644
220.0838
230.365
240.686
250.832
260.0121
270.222
280.335
290.353
30.261
300.393
310.378
325.47847e-9
330.523
340.166
350.618
360.149
370.0767
380.336
390.331
40.595
400.013
410.641
420.712
430.102
440.388
450.621
460.0481
470.12
480.0894
490.139
50.844
500.302
510.115
520.978
530.808
540.384
550.332
560.192
570.183
580.957
590.068
60.747
600.576
610.281
620.719
630.137
640.119
650.0468
660.258
670.989
680.14
690.182
70.605
700.922
710.051
720.955
730.104
740.877
750.26
760.436
770.0427
780.785
790.085
80.0394
800.886
810.461
820.282
830.946
840.352
850.211
860.946
870.341
880.294
890.24
90.368
900.948
910.264
920.941
930.262
940.319
950.209
960.589
970.643
980.357
990.00203



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: CNhs12127


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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