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FF:11751-123G5: 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 17:18, 29 March 2012


Name:mesenchymal precursor cell - bone marrow, donor2
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 precursor cell
cell lineNA
companyNA
collaborationClaudio Schneider LNCIB
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.0801
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-0.261
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: CNhs12367

Jaspar motifP-value
MA0002.20.774
MA0003.10.54
MA0004.10.645
MA0006.10.986
MA0007.10.703
MA0009.10.13
MA0014.10.955
MA0017.10.58
MA0018.20.0048
MA0019.10.308
MA0024.18.95678e-5
MA0025.15.01303e-4
MA0027.10.779
MA0028.10.582
MA0029.10.18
MA0030.10.0621
MA0031.10.271
MA0035.20.00299
MA0038.10.0922
MA0039.20.00425
MA0040.10.653
MA0041.10.423
MA0042.10.205
MA0043.10.0415
MA0046.10.126
MA0047.20.932
MA0048.10.0986
MA0050.10.665
MA0051.10.383
MA0052.10.671
MA0055.10.644
MA0057.10.573
MA0058.10.262
MA0059.10.643
MA0060.12.0357e-8
MA0061.10.112
MA0062.21.35642e-4
MA0065.20.377
MA0066.10.57
MA0067.10.23
MA0068.10.62
MA0069.10.243
MA0070.10.546
MA0071.10.316
MA0072.10.732
MA0073.10.895
MA0074.10.115
MA0076.10.525
MA0077.10.0109
MA0078.10.515
MA0079.20.672
MA0080.29.9838e-10
MA0081.10.0264
MA0083.16.39047e-11
MA0084.10.573
MA0087.10.823
MA0088.10.682
MA0090.19.24686e-4
MA0091.10.125
MA0092.10.744
MA0093.10.44
MA0099.20.73
MA0100.10.318
MA0101.10.0122
MA0102.20.639
MA0103.14.77417e-4
MA0104.20.79
MA0105.10.91
MA0106.10.28
MA0107.10.00431
MA0108.20.103
MA0111.10.274
MA0112.20.0384
MA0113.10.661
MA0114.10.408
MA0115.10.0224
MA0116.10.884
MA0117.10.511
MA0119.10.394
MA0122.10.586
MA0124.10.985
MA0125.10.064
MA0131.10.429
MA0135.10.444
MA0136.13.27273e-9
MA0137.20.0322
MA0138.20.534
MA0139.10.536
MA0140.10.059
MA0141.10.806
MA0142.10.153
MA0143.10.186
MA0144.10.155
MA0145.10.479
MA0146.10.479
MA0147.10.48
MA0148.10.51
MA0149.10.941
MA0150.10.804
MA0152.11.88283e-4
MA0153.10.331
MA0154.10.797
MA0155.10.518
MA0156.15.02425e-7
MA0157.10.63
MA0159.10.719
MA0160.10.21
MA0162.10.385
MA0163.10.107
MA0164.10.824
MA0258.10.493
MA0259.10.554



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: CNhs12367

Novel motifP-value
10.83
100.519
1000.819
1010.578
1020.00331
1030.352
1040.536
1050.278
1060.838
1070.878
1080.613
1090.829
110.96
1100.237
1110.658
1120.746
1130.00403
1140.277
1150.369
1160.275
1170.751
1180.412
1190.936
120.266
1200.881
1210.312
1220.0347
1232.31403e-5
1240.451
1250.961
1260.53
1270.722
1280.472
1290.726
130.702
1300.686
1310.624
1320.463
1330.889
1340.397
1350.776
1360.743
1370.56
1380.424
1390.737
140.62
1400.886
1410.101
1420.272
1430.872
1440.219
1450.762
1460.588
1470.0233
1480.933
1490.134
150.524
1500.868
1510.83
1520.536
1530.419
1540.68
1550.00563
1560.12
1570.36
1580.00555
1590.146
160.0537
1600.638
1610.615
1620.42
1630.865
1640.351
1650.655
1660.00564
1670.278
1680.406
1690.121
170.917
180.413
190.00399
20.972
200.852
210.563
220.322
230.492
240.126
250.189
260.622
270.732
280.492
290.219
30.697
300.337
310.632
324.0196e-13
330.713
340.391
350.67
360.0479
370.0216
380.237
390.216
40.0138
400.0303
410.188
420.341
430.758
440.519
450.991
460.633
470.0976
480.341
490.227
50.668
500.428
510.415
520.958
530.0304
540.635
550.0421
560.904
570.467
580.102
590.341
60.261
600.812
610.651
620.179
630.398
640.431
650.975
660.154
670.987
680.464
690.677
70.226
700.986
710.843
720.923
730.0762
740.128
750.919
760.458
770.0645
780.00275
790.003
80.697
800.379
810.923
820.747
830.894
840.805
850.908
860.229
870.698
880.234
890.0273
90.609
900.518
910.36
920.363
930.884
940.978
950.835
960.501
970.244
980.506
990.0359



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: CNhs12367


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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