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FF:13231-141I9: 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_rep3
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 numberF165
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-0.015
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-0.0996
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13421

Jaspar motifP-value
MA0002.20.358
MA0003.10.489
MA0004.10.391
MA0006.10.351
MA0007.10.346
MA0009.10.301
MA0014.10.354
MA0017.10.31
MA0018.22.73107e-6
MA0019.10.904
MA0024.11.37171e-4
MA0025.10.00104
MA0027.10.948
MA0028.10.0246
MA0029.10.286
MA0030.10.0415
MA0031.10.0161
MA0035.20.0294
MA0038.10.0599
MA0039.20.0286
MA0040.10.791
MA0041.10.604
MA0042.10.968
MA0043.11.35412e-4
MA0046.10.344
MA0047.20.289
MA0048.10.0496
MA0050.10.00191
MA0051.10.0618
MA0052.10.398
MA0055.10.661
MA0057.10.658
MA0058.10.448
MA0059.10.845
MA0060.14.03965e-8
MA0061.10.085
MA0062.23.75673e-7
MA0065.20.585
MA0066.10.51
MA0067.10.025
MA0068.10.107
MA0069.10.0354
MA0070.10.798
MA0071.10.97
MA0072.10.15
MA0073.10.873
MA0074.10.113
MA0076.10.0137
MA0077.10.456
MA0078.10.945
MA0079.20.445
MA0080.24.14267e-9
MA0081.10.00892
MA0083.12.58679e-4
MA0084.10.065
MA0087.10.939
MA0088.10.832
MA0090.10.00216
MA0091.10.0348
MA0092.10.153
MA0093.10.419
MA0099.20.0181
MA0100.10.233
MA0101.10.00132
MA0102.20.163
MA0103.11.3137e-4
MA0104.20.0735
MA0105.10.865
MA0106.10.325
MA0107.12.73983e-4
MA0108.20.237
MA0111.10.296
MA0112.20.00253
MA0113.10.37
MA0114.10.361
MA0115.10.0746
MA0116.10.147
MA0117.10.229
MA0119.10.248
MA0122.10.235
MA0124.10.193
MA0125.10.299
MA0131.10.361
MA0135.10.03
MA0136.15.55786e-11
MA0137.20.645
MA0138.20.327
MA0139.10.666
MA0140.10.214
MA0141.10.924
MA0142.10.0748
MA0143.10.789
MA0144.10.74
MA0145.10.121
MA0146.10.935
MA0147.10.14
MA0148.10.406
MA0149.10.698
MA0150.10.0491
MA0152.10.00217
MA0153.10.829
MA0154.10.669
MA0155.10.137
MA0156.11.19045e-8
MA0157.10.304
MA0159.10.62
MA0160.10.187
MA0162.10.0369
MA0163.10.0115
MA0164.10.72
MA0258.10.25
MA0259.10.277



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: CNhs13421

Novel motifP-value
10.981
100.443
1000.923
1010.414
1020.166
1030.829
1040.72
1050.251
1060.659
1070.217
1080.348
1090.752
110.703
1100.245
1110.626
1120.216
1130.0149
1140.258
1150.0307
1160.0713
1170.884
1180.295
1190.871
120.882
1200.727
1210.701
1220.0118
1238.60855e-4
1240.525
1250.689
1260.754
1270.527
1280.75
1290.788
130.925
1300.743
1310.886
1320.197
1330.785
1340.0202
1350.557
1360.55
1370.409
1380.293
1390.916
140.22
1400.722
1410.234
1420.646
1430.789
1440.319
1450.95
1460.819
1470.158
1480.477
1490.0169
150.397
1500.327
1510.647
1520.0925
1530.0465
1540.58
1550.00351
1560.552
1570.579
1580.00531
1590.565
160.0842
1600.425
1610.956
1620.232
1630.741
1640.159
1650.781
1660.134
1670.803
1680.735
1690.0237
170.79
180.183
199.42091e-4
20.177
200.196
210.0151
220.317
230.759
240.172
250.152
260.142
270.682
280.108
290.617
30.821
300.265
310.732
322.38337e-13
330.794
340.837
350.668
360.0341
370.0418
380.446
390.267
40.569
400.0812
410.237
420.453
430.873
440.263
450.765
460.524
470.695
480.927
490.62
50.876
500.67
510.847
520.739
530.175
540.677
550.123
560.981
570.671
580.128
590.141
60.359
600.964
610.842
620.525
630.563
640.986
650.538
660.238
670.578
680.418
690.418
70.293
700.64
710.368
720.988
730.0351
740.274
750.808
760.352
770.0431
780.377
790.00977
80.273
800.701
810.591
820.429
830.517
840.658
850.218
860.38
870.18
880.533
890.194
90.522
900.838
910.795
920.328
930.209
940.864
950.587
960.808
970.724
980.927
990.00912



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: CNhs13421


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

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