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FF:10045-101F9: 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 16:30, 29 March 2012


Name:kidney, fetal, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stage12-31 weeks fetus
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8082007A
catalog numberCat:636584
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Neural0.0222
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-0.0653
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-0.169
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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: CNhs10652

Jaspar motifP-value
MA0002.20.00208
MA0003.10.541
MA0004.10.561
MA0006.10.594
MA0007.10.36
MA0009.10.497
MA0014.10.969
MA0017.10.24
MA0018.20.235
MA0019.10.137
MA0024.10.72
MA0025.10.374
MA0027.10.826
MA0028.10.115
MA0029.10.67
MA0030.14.36491e-4
MA0031.10.147
MA0035.20.712
MA0038.10.0046
MA0039.20.252
MA0040.10.177
MA0041.10.142
MA0042.10.346
MA0043.10.546
MA0046.11.17514e-69
MA0047.20.465
MA0048.10.261
MA0050.10.396
MA0051.10.9
MA0052.10.0476
MA0055.10.366
MA0057.10.852
MA0058.10.623
MA0059.10.0186
MA0060.10.00277
MA0061.10.0128
MA0062.20.0342
MA0065.20.0704
MA0066.10.0311
MA0067.10.175
MA0068.19.10801e-6
MA0069.10.329
MA0070.10.298
MA0071.10.286
MA0072.10.368
MA0073.10.716
MA0074.10.738
MA0076.10.293
MA0077.10.623
MA0078.10.0964
MA0079.20.0568
MA0080.20.061
MA0081.10.276
MA0083.10.644
MA0084.10.496
MA0087.10.232
MA0088.10.0747
MA0090.10.0439
MA0091.10.307
MA0092.10.411
MA0093.10.656
MA0099.26.71236e-7
MA0100.10.462
MA0101.10.152
MA0102.20.857
MA0103.10.774
MA0104.20.0303
MA0105.11.65571e-8
MA0106.10.077
MA0107.10.234
MA0108.21.58659e-17
MA0111.10.266
MA0112.20.00349
MA0113.10.799
MA0114.10.898
MA0115.10.847
MA0116.17.59471e-5
MA0117.10.36
MA0119.10.0785
MA0122.10.457
MA0124.10.568
MA0125.10.0679
MA0131.10.936
MA0135.10.0135
MA0136.10.0351
MA0137.20.106
MA0138.20.447
MA0139.10.255
MA0140.10.606
MA0141.10.342
MA0142.10.672
MA0143.10.309
MA0144.10.851
MA0145.10.352
MA0146.10.287
MA0147.10.0109
MA0148.10.691
MA0149.10.0102
MA0150.10.00201
MA0152.10.418
MA0153.11.19775e-41
MA0154.10.00504
MA0155.10.53
MA0156.10.106
MA0157.10.772
MA0159.10.159
MA0160.10.219
MA0162.10.477
MA0163.13.20602e-13
MA0164.10.443
MA0258.10.0164
MA0259.10.24



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: CNhs10652

Novel motifP-value
10.0087
100.0129
1000.321
1010.446
1020.682
1030.0606
1040.747
1050.738
1060.212
1070.624
1080.517
1090.0164
110.035
1100.0835
1117.41935e-4
1120.147
1130.583
1143.6964e-4
1150.706
1160.303
1170.00817
1180.154
1190.101
120.791
1200.162
1210.924
1220.487
1230.00673
1240.637
1250.00375
1260.875
1270.111
1280.249
1290.901
130.135
1300.146
1310.722
1320.743
1330.899
1340.77
1350.89
1360.945
1370.269
1380.241
1390.0218
140.887
1400.181
1410.0922
1420.451
1430.00181
1440.495
1450.485
1460.612
1470.874
1480.00887
1490.468
150.0514
1500.404
1510.438
1520.945
1530.95
1540.378
1550.28
1560.769
1570.734
1580.435
1590.369
160.137
1600.365
1610.283
1620.691
1630.773
1640.0454
1650.45
1660.842
1670.0142
1680.93
1690.0536
170.23
180.0245
190.697
20.603
200.362
210.159
220.707
230.585
240.73
250.323
260.0172
270.725
280.768
290.0173
30.0501
300.112
310.874
320.122
330.318
340.463
350.0968
360.00828
370.0532
380.539
390.834
40.702
400.258
410.185
420.13
430.115
440.245
450.515
460.0262
470.0567
480.136
490.0676
50.21
500.835
510.543
520.618
530.577
540.684
550.149
560.73
570.182
580.453
590.457
60.348
600.424
610.273
620.132
630.255
640.147
650.454
660.753
670.21
680.431
690.57
70.435
700.00851
710.0146
720.581
730.093
740.202
750.00683
760.0417
770.859
780.243
790.0895
80.0451
800.578
810.117
820.188
830.583
840.563
850.208
860.21
870.185
880.941
890.223
90.944
900.042
910.409
920.246
930.156
940.0208
950.0767
960.12
970.742
980.0962
990.559



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: CNhs10652


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)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0001008 (renal system)
0001062 (anatomical entity)
0002100 (trunk)
0002113 (kidney)
0002417 (abdominal segment of trunk)
0003103 (compound organ)
0005095 (kidney rudiment)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006554 (urinary system structure)
0007687 (kidney field)

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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