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FF:11473-119C6: 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 16:38, 29 March 2012


Name:Adipocyte - omental, donor1
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
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.5
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-0.0974
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-0.381
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11054

Jaspar motifP-value
MA0002.20.111
MA0003.10.323
MA0004.10.148
MA0006.10.161
MA0007.10.225
MA0009.10.0749
MA0014.10.185
MA0017.10.302
MA0018.22.19295e-4
MA0019.10.48
MA0024.13.17883e-6
MA0025.10.0246
MA0027.10.631
MA0028.10.065
MA0029.10.692
MA0030.10.796
MA0031.10.688
MA0035.20.0368
MA0038.10.13
MA0039.20.00404
MA0040.10.222
MA0041.10.488
MA0042.10.671
MA0043.10.0251
MA0046.10.435
MA0047.20.639
MA0048.10.999
MA0050.10.00107
MA0051.10.296
MA0052.10.702
MA0055.10.181
MA0057.10.767
MA0058.10.105
MA0059.10.257
MA0060.11.72376e-7
MA0061.14.75088e-5
MA0062.28.29203e-7
MA0065.20.255
MA0066.10.883
MA0067.10.0585
MA0068.10.0509
MA0069.10.0345
MA0070.10.906
MA0071.10.988
MA0072.10.849
MA0073.10.957
MA0074.10.678
MA0076.10.0127
MA0077.10.318
MA0078.10.465
MA0079.20.759
MA0080.27.90806e-7
MA0081.10.0162
MA0083.17.18246e-5
MA0084.10.493
MA0087.10.575
MA0088.10.788
MA0090.15.78656e-8
MA0091.10.147
MA0092.10.00781
MA0093.10.158
MA0099.27.73522e-6
MA0100.10.938
MA0101.15.44188e-7
MA0102.20.45
MA0103.17.30434e-6
MA0104.20.00255
MA0105.14.05193e-4
MA0106.10.689
MA0107.13.16792e-6
MA0108.20.00395
MA0111.10.408
MA0112.20.111
MA0113.10.0347
MA0114.10.41
MA0115.10.00127
MA0116.10.366
MA0117.10.533
MA0119.10.268
MA0122.10.849
MA0124.10.318
MA0125.10.44
MA0131.10.289
MA0135.10.295
MA0136.11.34458e-8
MA0137.20.401
MA0138.20.183
MA0139.10.214
MA0140.10.297
MA0141.10.22
MA0142.10.0363
MA0143.10.962
MA0144.10.429
MA0145.10.15
MA0146.10.527
MA0147.10.00726
MA0148.10.369
MA0149.10.401
MA0150.10.0211
MA0152.10.00185
MA0153.10.728
MA0154.10.759
MA0155.10.291
MA0156.13.40913e-7
MA0157.10.481
MA0159.10.604
MA0160.10.062
MA0162.10.174
MA0163.10.435
MA0164.10.993
MA0258.10.655
MA0259.10.172



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: CNhs11054

Novel motifP-value
10.212
100.586
1000.917
1010.46
1020.0154
1030.977
1040.873
1050.111
1060.671
1070.552
1080.491
1090.25
110.258
1100.451
1110.581
1120.824
1130.0605
1140.759
1150.0604
1160.349
1170.135
1180.054
1190.0672
120.607
1200.306
1210.615
1220.255
1230.0083
1240.587
1250.157
1260.53
1270.0826
1280.692
1290.888
130.315
1300.392
1310.11
1320.475
1330.522
1340.303
1350.575
1360.449
1370.742
1380.167
1390.811
140.246
1400.17
1410.466
1420.382
1430.278
1440.936
1450.19
1460.998
1470.255
1480.93
1496.02375e-4
150.551
1500.766
1510.778
1520.0677
1530.127
1540.593
1550.017
1560.186
1570.698
1580.00148
1590.493
160.0468
1600.775
1610.122
1620.513
1630.0486
1640.754
1650.704
1660.0847
1670.274
1680.864
1690.0736
170.661
180.767
190.0233
20.161
200.204
210.606
220.344
230.464
240.358
250.307
260.341
270.814
280.169
290.113
30.742
300.285
310.951
326.27981e-12
330.511
340.919
350.748
360.0782
370.627
380.272
390.108
40.39
400.0802
410.759
420.3
430.839
440.774
450.84
460.411
470.44
480.37
490.398
50.486
500.696
510.398
520.614
530.146
540.842
550.64
560.311
570.76
580.415
590.431
60.541
600.954
610.221
620.427
630.884
640.232
650.773
660.142
670.673
680.916
690.736
70.386
700.673
710.73
720.358
730.139
740.347
750.515
760.201
770.155
780.271
790.257
80.47
800.601
810.846
820.898
830.649
840.0987
850.0677
860.414
870.273
880.684
890.456
90.391
900.891
910.384
920.344
930.964
940.423
950.494
960.838
970.288
980.231
990.0689



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: CNhs11054


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)
0000136 (fat cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002615 (adipocyte of omentum tissue)

UBERON: Anatomy
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001178 (visceral peritoneum)
0002050 (embryonic structure)
0002100 (trunk)
0002323 (body cavity)
0002358 (peritoneum)
0002384 (connective tissue)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003684 (abdominal cavity)
0003688 (omentum)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004923 (organ component layer)
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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