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FF:11474-119C7: 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 17:10, 29 March 2012


Name:Adipocyte - omental, donor2
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-v1.6
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-penis0.131
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-0.363
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: CNhs12067

Jaspar motifP-value
MA0002.20.858
MA0003.10.173
MA0004.10.583
MA0006.10.118
MA0007.10.101
MA0009.10.295
MA0014.10.819
MA0017.10.897
MA0018.22.23748e-5
MA0019.10.248
MA0024.15.42756e-6
MA0025.14.98666e-4
MA0027.10.386
MA0028.10.00366
MA0029.10.294
MA0030.10.186
MA0031.10.437
MA0035.20.218
MA0038.10.0623
MA0039.20.0954
MA0040.10.248
MA0041.10.461
MA0042.10.598
MA0043.12.46525e-5
MA0046.10.222
MA0047.20.72
MA0048.10.605
MA0050.18.19464e-6
MA0051.10.00225
MA0052.10.357
MA0055.10.953
MA0057.10.175
MA0058.10.395
MA0059.10.549
MA0060.18.95356e-7
MA0061.10.198
MA0062.21.25066e-8
MA0065.20.333
MA0066.10.0902
MA0067.10.0531
MA0068.10.519
MA0069.10.217
MA0070.10.879
MA0071.10.34
MA0072.10.831
MA0073.10.874
MA0074.10.746
MA0076.12.70482e-5
MA0077.10.445
MA0078.10.657
MA0079.20.853
MA0080.21.93221e-6
MA0081.10.00151
MA0083.10.00826
MA0084.10.96
MA0087.10.452
MA0088.10.623
MA0090.14.18393e-4
MA0091.10.0279
MA0092.10.00416
MA0093.10.435
MA0099.25.77853e-5
MA0100.10.352
MA0101.10.00273
MA0102.20.178
MA0103.10.112
MA0104.20.115
MA0105.10.98
MA0106.10.3
MA0107.10.00584
MA0108.20.0435
MA0111.10.928
MA0112.24.21003e-5
MA0113.10.0951
MA0114.10.65
MA0115.10.0155
MA0116.10.13
MA0117.10.188
MA0119.10.0925
MA0122.10.862
MA0124.10.04
MA0125.10.225
MA0131.10.0809
MA0135.10.197
MA0136.12.51438e-10
MA0137.20.432
MA0138.20.00661
MA0139.10.587
MA0140.10.675
MA0141.10.695
MA0142.10.586
MA0143.10.462
MA0144.10.519
MA0145.10.0762
MA0146.10.637
MA0147.10.247
MA0148.10.507
MA0149.10.889
MA0150.10.0819
MA0152.10.0414
MA0153.10.893
MA0154.10.111
MA0155.10.053
MA0156.11.1149e-9
MA0157.10.972
MA0159.10.107
MA0160.10.734
MA0162.10.0507
MA0163.10.0441
MA0164.10.788
MA0258.10.0215
MA0259.10.364



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: CNhs12067

Novel motifP-value
10.563
100.825
1000.822
1010.328
1020.0778
1030.238
1040.798
1050.108
1060.049
1070.0892
1080.158
1090.373
110.356
1100.279
1110.258
1120.294
1130.713
1140.158
1150.00501
1160.148
1170.838
1180.684
1190.361
120.358
1200.514
1210.289
1220.333
1230.133
1240.841
1250.934
1260.717
1270.747
1280.179
1290.46
130.856
1300.972
1310.809
1320.136
1330.866
1340.701
1350.235
1360.744
1370.789
1380.69
1390.117
140.429
1400.872
1410.918
1420.736
1430.575
1440.881
1450.78
1460.759
1470.0676
1480.727
1492.51059e-4
150.708
1500.569
1510.745
1520.0312
1530.548
1540.991
1550.2
1560.973
1570.718
1580.137
1590.821
160.0218
1600.1
1610.75
1620.64
1630.872
1640.439
1650.98
1660.355
1670.314
1680.837
1690.0163
170.27
180.21
190.00735
20.311
200.387
210.356
220.126
230.0268
240.466
250.484
260.455
270.105
280.23
290.67
30.337
300.507
310.405
322.48961e-12
330.868
340.733
350.46
360.119
370.13
380.769
390.141
40.922
400.652
410.859
420.641
430.14
440.185
450.656
460.259
470.582
480.767
490.405
50.32
500.668
510.815
520.424
530.339
540.754
550.371
560.846
570.406
580.796
590.0407
60.566
600.384
610.363
620.612
630.158
640.7
650.0778
660.159
670.568
680.204
690.284
70.792
700.291
710.525
720.879
730.0272
740.215
750.442
760.449
770.0047
780.767
790.0203
80.159
800.769
810.361
820.0746
830.999
840.0689
850.00121
860.579
870.307
880.43
890.0138
90.32
900.67
910.634
920.0306
930.932
940.535
950.403
960.502
970.29
980.471
990.032



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: CNhs12067


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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