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FF:10010-101C1: 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 16:12, 29 March 2012


Name:adipose tissue, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueadipose tissue
dev stage65,65,76 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -1
catalog numberCat:AM6000 Lot:0910061 -1
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
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-penis0.0404
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.0594
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs10615

Jaspar motifP-value
MA0002.20.122
MA0003.10.157
MA0004.10.307
MA0006.10.344
MA0007.10.444
MA0009.10.199
MA0014.10.261
MA0017.10.193
MA0018.20.0875
MA0019.10.0174
MA0024.10.0242
MA0025.10.913
MA0027.10.554
MA0028.11.67532e-6
MA0029.10.569
MA0030.10.011
MA0031.10.003
MA0035.20.238
MA0038.10.406
MA0039.20.933
MA0040.10.367
MA0041.10.0723
MA0042.10.133
MA0043.10.293
MA0046.10.544
MA0047.20.0578
MA0048.10.0162
MA0050.11.07754e-4
MA0051.10.00717
MA0052.11.29901e-11
MA0055.14.32924e-5
MA0057.10.795
MA0058.10.358
MA0059.10.0292
MA0060.13.71016e-5
MA0061.10.00665
MA0062.23.91524e-8
MA0065.20.466
MA0066.10.232
MA0067.10.459
MA0068.13.46449e-4
MA0069.10.845
MA0070.10.551
MA0071.10.327
MA0072.10.794
MA0073.10.928
MA0074.10.844
MA0076.13.15592e-7
MA0077.10.854
MA0078.10.0815
MA0079.20.239
MA0080.20.00171
MA0081.10.265
MA0083.10.00135
MA0084.10.673
MA0087.10.225
MA0088.10.0504
MA0090.10.0361
MA0091.10.414
MA0092.10.129
MA0093.10.259
MA0099.22.89192e-6
MA0100.10.421
MA0101.10.0897
MA0102.20.404
MA0103.10.00245
MA0104.20.0108
MA0105.17.35399e-5
MA0106.10.0907
MA0107.10.0838
MA0108.21.56709e-12
MA0111.10.895
MA0112.20.654
MA0113.10.024
MA0114.10.375
MA0115.10.731
MA0116.10.0146
MA0117.10.231
MA0119.10.657
MA0122.10.208
MA0124.10.214
MA0125.10.926
MA0131.10.378
MA0135.10.46
MA0136.10.155
MA0137.25.15049e-7
MA0138.20.271
MA0139.10.019
MA0140.10.189
MA0141.10.298
MA0142.10.0408
MA0143.10.746
MA0144.13.61999e-4
MA0145.10.0244
MA0146.10.203
MA0147.10.00418
MA0148.10.0486
MA0149.10.225
MA0150.10.0282
MA0152.10.343
MA0153.10.264
MA0154.10.924
MA0155.10.304
MA0156.10.606
MA0157.10.0336
MA0159.10.676
MA0160.10.62
MA0162.10.749
MA0163.16.74361e-6
MA0164.10.26
MA0258.10.143
MA0259.10.0717



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: CNhs10615

Novel motifP-value
10.0672
100.178
1000.0753
1010.516
1020.348
1030.447
1040.437
1050.529
1060.42
1070.0862
1080.92
1090.0958
110.18
1100.256
1110.112
1120.859
1130.343
1140.174
1150.258
1160.637
1170.00751
1180.00952
1190.622
120.867
1200.0428
1210.433
1220.619
1230.00409
1240.765
1250.323
1260.695
1270.463
1280.637
1290.704
130.206
1300.728
1310.6
1320.157
1330.135
1340.582
1350.0802
1360.95
1370.48
1380.827
1390.939
140.685
1400.0161
1410.522
1420.417
1430.0327
1440.857
1450.435
1460.251
1470.274
1480.454
1490.262
150.125
1500.902
1510.896
1520.186
1530.152
1540.465
1550.213
1560.896
1570.693
1580.304
1590.966
160.684
1600.725
1610.391
1620.921
1630.667
1640.0622
1650.161
1660.967
1670.0399
1680.604
1690.838
170.737
180.2
190.127
20.0833
200.0421
210.997
220.585
230.113
240.899
250.494
260.111
270.672
280.459
290.0309
30.371
300.0956
310.868
320.414
330.355
340.112
350.402
360.103
370.381
380.828
390.009
40.0794
400.0686
410.766
420.244
430.568
440.328
450.153
460.266
470.123
480.178
490.0782
50.916
500.425
510.852
520.222
530.887
540.819
550.634
560.607
570.136
580.695
590.542
60.554
600.395
610.388
620.757
630.932
640.126
650.749
660.0177
670.389
680.282
690.213
70.712
700.279
710.0811
720.453
730.684
740.949
750.0253
760.0722
770.091
780.547
790.408
80.404
800.305
810.78
820.997
830.278
840.519
850.226
860.875
870.173
880.809
890.671
90.193
900.548
910.305
920.415
930.179
940.176
950.0133
960.983
970.308
980.532
990.435



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: CNhs10615


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

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0001013 (adipose tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0007023 (adult organism)

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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