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FF:11476-119C9: 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 - perirenal, 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-v1.8
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
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-0.465
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: CNhs12069

Jaspar motifP-value
MA0002.20.561
MA0003.10.226
MA0004.10.551
MA0006.10.381
MA0007.10.177
MA0009.10.613
MA0014.10.715
MA0017.10.745
MA0018.22.94019e-5
MA0019.10.557
MA0024.14.58037e-5
MA0025.10.00148
MA0027.10.704
MA0028.10.0556
MA0029.10.545
MA0030.10.0698
MA0031.10.183
MA0035.20.148
MA0038.10.00384
MA0039.20.0705
MA0040.10.263
MA0041.10.597
MA0042.10.762
MA0043.18.83031e-4
MA0046.10.226
MA0047.20.845
MA0048.10.581
MA0050.14.80871e-5
MA0051.10.00933
MA0052.10.153
MA0055.10.876
MA0057.10.186
MA0058.10.306
MA0059.10.402
MA0060.11.16179e-9
MA0061.10.392
MA0062.24.2275e-6
MA0065.20.501
MA0066.10.0827
MA0067.10.00971
MA0068.10.41
MA0069.10.158
MA0070.10.63
MA0071.10.358
MA0072.11
MA0073.10.869
MA0074.10.456
MA0076.10.00223
MA0077.10.136
MA0078.10.525
MA0079.20.548
MA0080.22.72753e-6
MA0081.10.0194
MA0083.10.016
MA0084.10.918
MA0087.10.791
MA0088.10.768
MA0090.12.0108e-4
MA0091.10.0228
MA0092.10.014
MA0093.10.414
MA0099.23.25273e-4
MA0100.10.278
MA0101.10.00715
MA0102.20.138
MA0103.10.369
MA0104.20.333
MA0105.10.465
MA0106.10.0266
MA0107.10.00833
MA0108.20.107
MA0111.10.812
MA0112.26.09655e-5
MA0113.10.112
MA0114.10.585
MA0115.10.0165
MA0116.10.049
MA0117.10.521
MA0119.10.0292
MA0122.10.777
MA0124.10.0167
MA0125.10.144
MA0131.10.166
MA0135.10.385
MA0136.12.54449e-10
MA0137.20.404
MA0138.20.148
MA0139.10.368
MA0140.10.67
MA0141.10.453
MA0142.10.217
MA0143.10.541
MA0144.10.366
MA0145.10.202
MA0146.10.455
MA0147.10.609
MA0148.10.585
MA0149.10.963
MA0150.10.0652
MA0152.10.0555
MA0153.10.529
MA0154.10.0647
MA0155.10.238
MA0156.12.61994e-7
MA0157.10.972
MA0159.10.0103
MA0160.10.489
MA0162.10.0177
MA0163.13.7617e-4
MA0164.10.804
MA0258.10.0168
MA0259.10.927



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: CNhs12069

Novel motifP-value
10.42
100.447
1000.886
1010.314
1020.187
1030.0857
1040.942
1050.162
1060.056
1070.0288
1080.249
1090.163
110.347
1100.237
1110.537
1120.141
1130.327
1140.104
1150.0221
1160.0692
1170.88
1180.438
1190.598
120.37
1200.241
1210.155
1220.348
1230.398
1240.915
1250.606
1260.994
1270.553
1280.175
1290.701
130.87
1300.606
1310.569
1320.46
1330.285
1340.692
1350.365
1360.637
1370.486
1380.906
1390.0775
140.522
1400.942
1410.649
1420.841
1430.466
1440.865
1450.911
1460.849
1470.128
1480.516
1492.5048e-4
150.556
1500.738
1510.483
1520.0854
1530.613
1540.674
1550.157
1560.558
1570.685
1580.122
1590.652
160.0115
1600.137
1610.755
1620.918
1630.567
1640.149
1650.924
1660.103
1670.829
1680.673
1690.0107
170.203
180.111
190.00932
20.319
200.599
210.91
220.106
230.0595
240.45
250.976
260.574
270.197
280.308
290.447
30.312
300.593
310.317
322.2671e-12
330.876
340.811
350.422
360.712
370.104
380.688
390.235
40.864
400.422
410.957
420.757
430.11
440.0653
450.758
460.191
470.452
480.591
490.357
50.422
500.725
510.73
520.59
530.361
540.645
550.353
560.91
570.375
580.949
590.0396
60.624
600.245
610.694
620.37
630.141
640.495
650.148
660.124
670.381
680.813
690.264
70.779
700.0232
710.256
720.626
730.0457
740.162
750.43
760.935
770.024
780.797
790.0106
80.0756
800.832
810.333
820.0521
830.974
840.165
850.00616
860.48
870.646
880.152
890.0101
90.573
900.661
910.275
920.0191
930.312
940.281
950.308
960.895
970.34
980.256
990.056



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: CNhs12069


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)
0002616 (perirenal adipocyte cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001013 (adipose tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0005406 (perirenal fat)

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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