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FF:10017-101C8: 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 16:26, 29 March 2012


Name:kidney, 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
tissuekidney
dev stage60,62,63 years old adult
sexfemale
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 -8
catalog numberCat:AM6000 Lot:0910061 -8
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-penis0.103
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-0.326
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10622

Jaspar motifP-value
MA0002.20.052
MA0003.10.192
MA0004.10.323
MA0006.10.0422
MA0007.10.275
MA0009.10.666
MA0014.10.172
MA0017.14.21675e-11
MA0018.20.0559
MA0019.10.0222
MA0024.10.00712
MA0025.10.698
MA0027.10.474
MA0028.10.0623
MA0029.10.258
MA0030.10.0586
MA0031.10.266
MA0035.20.794
MA0038.10.107
MA0039.20.0431
MA0040.10.682
MA0041.10.297
MA0042.10.852
MA0043.10.16
MA0046.18.71508e-124
MA0047.20.93
MA0048.10.0134
MA0050.10.31
MA0051.10.178
MA0052.10.551
MA0055.10.0803
MA0057.10.486
MA0058.10.535
MA0059.10.0251
MA0060.10.51
MA0061.12.37833e-4
MA0062.20.01
MA0065.20.124
MA0066.10.386
MA0067.10.00458
MA0068.10.003
MA0069.10.13
MA0070.10.758
MA0071.10.423
MA0072.10.466
MA0073.10.983
MA0074.10.446
MA0076.10.133
MA0077.10.53
MA0078.10.00218
MA0079.20.0555
MA0080.20.233
MA0081.10.147
MA0083.10.869
MA0084.10.54
MA0087.10.111
MA0088.10.21
MA0090.10.0047
MA0091.10.572
MA0092.10.785
MA0093.10.389
MA0099.21.24127e-13
MA0100.10.108
MA0101.10.00673
MA0102.20.939
MA0103.10.00227
MA0104.20.00118
MA0105.16.69791e-6
MA0106.10.192
MA0107.10.0108
MA0108.21.31865e-5
MA0111.10.348
MA0112.20.713
MA0113.10.0935
MA0114.11.60594e-8
MA0115.10.0043
MA0116.10.0282
MA0117.10.0846
MA0119.10.274
MA0122.10.226
MA0124.10.769
MA0125.10.253
MA0131.10.378
MA0135.10.116
MA0136.10.217
MA0137.24.85894e-5
MA0138.20.522
MA0139.10.612
MA0140.10.162
MA0141.10.0591
MA0142.10.912
MA0143.10.392
MA0144.10.016
MA0145.10.00107
MA0146.10.673
MA0147.12.36174e-4
MA0148.10.285
MA0149.10.312
MA0150.10.00707
MA0152.10.106
MA0153.17.50836e-70
MA0154.10.151
MA0155.10.559
MA0156.10.0721
MA0157.10.763
MA0159.10.143
MA0160.10.362
MA0162.10.804
MA0163.12.26051e-5
MA0164.10.147
MA0258.10.44
MA0259.10.0227



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: CNhs10622

Novel motifP-value
10.192
100.0493
1000.618
1010.335
1020.122
1030.147
1040.463
1050.937
1060.873
1070.194
1080.998
1090.1
110.155
1100.0925
1110.0167
1120.443
1130.779
1140.0136
1150.827
1160.156
1170.00966
1180.162
1190.635
120.968
1200.144
1210.415
1220.423
1230.0049
1240.595
1258.94152e-4
1260.175
1270.122
1280.85
1290.688
130.327
1300.437
1310.548
1320.626
1330.269
1340.573
1350.397
1360.651
1370.377
1380.513
1390.169
140.621
1400.657
1410.154
1420.998
1430.00967
1440.364
1450.823
1460.0614
1470.776
1480.44
1490.387
150.136
1500.614
1510.713
1520.126
1530.402
1540.173
1550.799
1560.473
1570.468
1580.173
1590.643
160.877
1600.286
1610.251
1620.622
1630.791
1640.0548
1650.402
1660.433
1670.0321
1680.249
1690.472
170.446
180.00109
190.492
20.172
200.305
210.0795
220.79
230.85
240.618
250.41
260.137
270.729
280.924
290.0137
30.147
300.0309
310.939
320.023
330.845
340.416
350.132
360.0226
370.305
380.757
390.213
40.217
400.313
410.0654
420.153
430.336
440.534
450.187
460.137
470.386
480.574
490.0514
50.417
500.779
510.402
520.0965
530.572
540.798
550.989
560.741
570.197
580.862
590.831
60.231
600.728
610.737
620.459
630.611
640.254
650.963
660.317
670.103
680.263
690.632
70.789
700.122
710.0219
720.833
730.775
740.614
750.0183
760.0125
770.0537
780.451
790.0451
80.418
800.103
810.262
820.878
830.991
840.326
850.682
860.571
870.648
880.753
890.855
90.517
900.549
910.373
920.678
930.273
940.0376
950.189
960.825
970.421
980.32
990.158



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: CNhs10622


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)
0007023 (adult organism)
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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