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FF:13230-141I8: 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 17:32, 29 March 2012


Name:mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age16
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationPeter Arner(Karolinska)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberF164
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-penis-0.00594
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-0.099
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs13420

Jaspar motifP-value
MA0002.20.582
MA0003.10.408
MA0004.10.294
MA0006.10.268
MA0007.10.875
MA0009.10.345
MA0014.10.23
MA0017.10.434
MA0018.27.25204e-7
MA0019.10.543
MA0024.10.00641
MA0025.10.00134
MA0027.10.701
MA0028.10.102
MA0029.10.575
MA0030.10.0117
MA0031.10.0057
MA0035.20.0091
MA0038.10.0457
MA0039.20.0538
MA0040.10.743
MA0041.10.586
MA0042.10.845
MA0043.11.57956e-5
MA0046.10.244
MA0047.20.129
MA0048.10.0792
MA0050.10.0134
MA0051.10.217
MA0052.10.215
MA0055.10.671
MA0057.10.487
MA0058.10.284
MA0059.10.546
MA0060.16.60124e-9
MA0061.10.515
MA0062.23.08119e-6
MA0065.20.933
MA0066.10.31
MA0067.10.0158
MA0068.10.338
MA0069.10.0135
MA0070.10.733
MA0071.10.515
MA0072.10.297
MA0073.10.774
MA0074.10.115
MA0076.10.0341
MA0077.10.231
MA0078.10.933
MA0079.20.167
MA0080.21.79627e-8
MA0081.10.00941
MA0083.13.67834e-4
MA0084.10.0638
MA0087.10.768
MA0088.10.551
MA0090.10.00218
MA0091.10.0124
MA0092.10.0612
MA0093.10.283
MA0099.20.0315
MA0100.10.198
MA0101.10.00341
MA0102.20.0931
MA0103.13.18176e-4
MA0104.20.228
MA0105.10.154
MA0106.10.0757
MA0107.19.60855e-4
MA0108.20.615
MA0111.10.448
MA0112.23.45079e-4
MA0113.10.345
MA0114.10.538
MA0115.10.0174
MA0116.10.024
MA0117.10.526
MA0119.10.119
MA0122.10.525
MA0124.10.239
MA0125.10.784
MA0131.10.4
MA0135.10.161
MA0136.11.51265e-11
MA0137.20.745
MA0138.20.198
MA0139.10.828
MA0140.10.13
MA0141.10.423
MA0142.10.225
MA0143.10.793
MA0144.10.342
MA0145.10.0677
MA0146.10.942
MA0147.10.374
MA0148.10.178
MA0149.10.677
MA0150.10.0493
MA0152.16.96406e-4
MA0153.10.913
MA0154.10.22
MA0155.10.245
MA0156.12.1381e-8
MA0157.10.211
MA0159.10.207
MA0160.10.231
MA0162.10.0585
MA0163.10.00343
MA0164.10.759
MA0258.10.138
MA0259.10.394



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: CNhs13420

Novel motifP-value
10.396
100.364
1000.691
1010.672
1020.166
1030.363
1040.724
1050.332
1060.456
1070.183
1080.2
1090.766
110.522
1100.164
1110.94
1120.158
1130.016
1140.231
1150.0789
1160.0743
1170.556
1180.536
1190.879
120.679
1200.621
1210.832
1220.00746
1230.0102
1240.357
1250.729
1260.987
1270.827
1280.345
1290.829
130.615
1300.728
1310.502
1320.282
1330.579
1340.0569
1350.807
1360.308
1370.289
1380.443
1390.898
140.248
1400.565
1410.66
1420.812
1430.878
1440.2
1450.512
1460.663
1470.304
1480.558
1490.00849
150.559
1500.255
1510.748
1520.219
1530.139
1540.865
1550.00209
1560.793
1570.463
1580.011
1590.281
160.0315
1600.189
1610.885
1620.355
1630.876
1640.135
1650.945
1660.0642
1670.977
1680.772
1690.0127
170.592
180.0992
190.00312
20.244
200.372
210.0101
220.292
230.643
240.297
250.355
260.154
270.696
280.165
290.515
30.309
300.215
310.5
328.20912e-14
330.94
340.612
350.997
360.0833
370.0574
380.643
390.12
40.277
400.238
410.353
420.846
430.428
440.125
450.928
460.275
470.994
480.743
490.924
50.9
500.78
510.862
520.865
530.126
540.582
550.146
560.878
570.95
580.423
590.0926
60.734
600.833
610.923
620.796
630.432
640.946
650.448
660.211
670.342
680.377
690.672
70.29
700.277
710.172
720.607
730.124
740.115
750.443
760.563
770.0117
780.52
790.00322
80.121
800.844
810.4
820.382
830.699
840.762
850.424
860.397
870.133
880.579
890.047
90.532
900.83
910.771
920.338
930.225
940.566
950.79
960.686
970.832
980.983
990.0352



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: CNhs13420


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)
0002570 (mesenchymal stem cell of adipose)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001013 (adipose tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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