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FF:11536-120A6: 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:Mesenchymal Stem Cells - bone marrow, donor1
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 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 numberSC7505
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-0.0916
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-lymphoma0.183
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: CNhs11344

Jaspar motifP-value
MA0002.20.471
MA0003.10.366
MA0004.10.574
MA0006.10.309
MA0007.10.017
MA0009.10.424
MA0014.10.899
MA0017.10.194
MA0018.20.0374
MA0019.10.449
MA0024.10.0107
MA0025.10.0758
MA0027.10.468
MA0028.10.31
MA0029.10.168
MA0030.19.05722e-4
MA0031.12.83655e-4
MA0035.20.84
MA0038.12.42735e-4
MA0039.20.456
MA0040.10.776
MA0041.10.44
MA0042.10.802
MA0043.18.73383e-4
MA0046.10.0805
MA0047.20.0934
MA0048.10.0508
MA0050.11.53536e-9
MA0051.19.1648e-6
MA0052.10.528
MA0055.10.00162
MA0057.10.243
MA0058.10.611
MA0059.10.214
MA0060.15.29872e-12
MA0061.10.882
MA0062.20.598
MA0065.20.135
MA0066.10.116
MA0067.10.00577
MA0068.10.425
MA0069.10.0869
MA0070.10.0145
MA0071.10.0888
MA0072.10.345
MA0073.10.809
MA0074.10.719
MA0076.10.985
MA0077.10.601
MA0078.10.735
MA0079.20.892
MA0080.23.85109e-6
MA0081.10.00875
MA0083.10.0087
MA0084.10.889
MA0087.10.914
MA0088.10.0288
MA0090.10.0913
MA0091.10.335
MA0092.10.558
MA0093.10.657
MA0099.20.00599
MA0100.10.542
MA0101.10.26
MA0102.21.49661e-6
MA0103.10.0429
MA0104.20.743
MA0105.10.377
MA0106.10.0897
MA0107.10.125
MA0108.20.0174
MA0111.10.394
MA0112.20.0144
MA0113.10.0422
MA0114.10.0624
MA0115.10.92
MA0116.10.135
MA0117.10.54
MA0119.10.161
MA0122.10.74
MA0124.10.01
MA0125.10.132
MA0131.10.785
MA0135.10.286
MA0136.19.23987e-6
MA0137.20.221
MA0138.20.349
MA0139.10.558
MA0140.10.337
MA0141.10.0503
MA0142.10.398
MA0143.10.75
MA0144.10.643
MA0145.10.325
MA0146.10.034
MA0147.10.564
MA0148.10.28
MA0149.10.381
MA0150.10.812
MA0152.10.371
MA0153.10.397
MA0154.10.178
MA0155.10.239
MA0156.10.0223
MA0157.10.0419
MA0159.10.811
MA0160.10.251
MA0162.10.212
MA0163.10.0379
MA0164.10.919
MA0258.10.23
MA0259.10.825



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: CNhs11344

Novel motifP-value
10.506
100.802
1000.381
1010.664
1020.609
1030.414
1040.393
1050.205
1060.794
1070.0908
1080.915
1090.0123
110.0251
1100.0571
1110.602
1120.653
1130.661
1140.767
1150.395
1160.0321
1170.37
1180.771
1190.815
120.598
1200.188
1210.327
1220.636
1230.00605
1240.624
1250.894
1260.585
1270.638
1280.794
1290.856
130.205
1300.0074
1310.367
1320.26
1330.403
1340.0532
1350.917
1360.986
1370.0594
1380.175
1390.231
140.926
1400.677
1410.426
1420.203
1430.273
1440.756
1450.446
1460.0249
1470.281
1480.734
1490.435
150.913
1500.302
1510.637
1520.314
1530.178
1540.14
1550.65
1560.585
1570.747
1580.132
1590.493
160.314
1600.0178
1610.278
1620.444
1630.319
1640.807
1650.645
1660.826
1670.417
1680.737
1690.0745
170.459
180.241
190.0353
20.661
200.755
210.337
220.0778
230.92
240.659
250.921
260.0439
270.481
280.0981
290.552
30.353
300.159
310.471
320.00475
330.194
340.264
350.633
360.291
370.147
380.422
390.339
40.402
400.0278
410.544
420.556
430.35
440.357
450.473
460.0817
470.0756
480.0786
490.191
50.896
500.149
510.466
520.786
530.431
540.645
550.806
560.195
570.336
580.327
590.0287
60.625
600.66
610.503
620.421
630.113
640.117
650.0932
660.023
670.823
680.0762
690.0998
70.587
700.438
710.0634
720.625
730.0761
740.864
750.438
760.207
770.0719
780.965
790.858
80.0322
800.726
810.973
820.908
830.56
840.499
850.424
860.703
870.133
880.284
890.0649
90.416
900.126
910.173
920.685
930.61
940.486
950.113
960.556
970.771
980.658
992.84549e-5



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: CNhs11344


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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