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|rna_box=122
|rna_box=122

Revision as of 15:25, 21 September 2012


Name:Renal Epithelial Cells, donor3
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 stageNA
sexNA
ageNA
cell typeepithelial cell of kidney
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2265
catalog numberSC4125
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-penis-0.146
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-lymphoma0.251
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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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



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: CNhs12732

Jaspar motifP-value
MA0002.20.0541
MA0003.10.97
MA0004.10.0255
MA0006.10.0293
MA0007.10.545
MA0009.10.0625
MA0014.10.205
MA0017.10.917
MA0018.20.962
MA0019.10.102
MA0024.10.0274
MA0025.10.964
MA0027.10.646
MA0028.10.51
MA0029.10.951
MA0030.10.814
MA0031.10.278
MA0035.20.411
MA0038.10.00581
MA0039.20.0187
MA0040.10.548
MA0041.10.573
MA0042.10.591
MA0043.10.738
MA0046.14.78681e-27
MA0047.20.383
MA0048.10.35
MA0050.10.00591
MA0051.10.503
MA0052.10.373
MA0055.10.438
MA0057.10.611
MA0058.10.00215
MA0059.10.0728
MA0060.10.00102
MA0061.10.802
MA0062.24.68479e-4
MA0065.20.395
MA0066.10.921
MA0067.10.0223
MA0068.10.199
MA0069.10.245
MA0070.10.0482
MA0071.10.525
MA0072.10.557
MA0073.10.905
MA0074.10.937
MA0076.10.0237
MA0077.10.0152
MA0078.10.887
MA0079.20.822
MA0080.25.14599e-7
MA0081.10.00561
MA0083.10.215
MA0084.10.0845
MA0087.10.927
MA0088.10.484
MA0090.10.00355
MA0091.10.00104
MA0092.10.211
MA0093.10.0317
MA0099.20.00142
MA0100.10.647
MA0101.10.394
MA0102.20.138
MA0103.11.38242e-5
MA0104.20.0162
MA0105.10.0891
MA0106.10.0602
MA0107.10.364
MA0108.20.0315
MA0111.10.507
MA0112.20.0838
MA0113.10.118
MA0114.10.659
MA0115.10.716
MA0116.10.00901
MA0117.10.298
MA0119.10.0686
MA0122.10.362
MA0124.10.272
MA0125.10.207
MA0131.10.34
MA0135.10.253
MA0136.11.05081e-4
MA0137.20.93
MA0138.20.0821
MA0139.10.836
MA0140.10.073
MA0141.10.0212
MA0142.10.216
MA0143.10.785
MA0144.10.788
MA0145.10.0791
MA0146.10.432
MA0147.10.0246
MA0148.10.136
MA0149.10.302
MA0150.10.0968
MA0152.10.251
MA0153.18.36236e-23
MA0154.10.266
MA0155.10.827
MA0156.10.0018
MA0157.10.308
MA0159.10.69
MA0160.10.0484
MA0162.10.254
MA0163.19.28295e-4
MA0164.10.731
MA0258.10.021
MA0259.10.206



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: CNhs12732

Novel motifP-value
10.0645
100.00927
1000.948
1010.0443
1020.458
1030.796
1040.786
1050.944
1060.805
1070.0562
1080.816
1090.26
110.125
1100.128
1110.412
1120.187
1130.328
1140.00112
1150.236
1160.245
1170.0402
1180.588
1190.952
120.106
1200.375
1210.614
1220.288
1230.00788
1240.125
1250.439
1260.731
1270.306
1280.741
1290.132
130.703
1300.21
1310.205
1320.15
1330.0978
1340.234
1350.447
1360.533
1370.0945
1380.217
1393.36072e-4
140.782
1400.264
1410.244
1420.445
1430.629
1440.919
1450.831
1460.248
1470.477
1480.119
1490.678
150.418
1500.971
1510.526
1520.0695
1530.61
1540.416
1550.357
1560.8
1570.655
1580.203
1590.749
160.747
1600.736
1610.485
1620.432
1630.343
1640.237
1650.307
1660.789
1670.738
1680.788
1690.535
170.593
180.166
190.11
20.771
200.885
210.296
220.609
230.545
240.514
250.433
260.0996
270.871
280.789
290.634
30.164
300.0748
310.876
320.0172
330.195
340.509
350.00139
360.42
370.676
380.759
390.331
40.571
400.309
410.0415
420.344
430.162
440.347
450.391
460.0763
470.473
480.494
490.0343
50.302
500.421
510.946
520.618
530.181
540.834
550.0361
560.483
570.344
580.184
590.885
60.206
600.394
610.4
620.0482
630.934
640.2
650.548
660.133
670.325
680.0828
690.738
70.313
700.00382
710.0294
720.912
730.753
740.192
750.068
760.129
770.521
780.483
790.824
80.322
800.153
810.0406
820.0934
830.256
840.935
850.02
860.151
870.37
880.996
890.635
90.4
900.874
910.198
920.365
930.379
940.155
950.603
960.631
970.908
980.0191
990.0124



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: CNhs12732


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
1000497 (kidney cell)
0002518 (kidney epithelial cell)
1000449 (epithelial cell of nephron)
1000507 (kidney tubule cell)
1000494 (nephron tubule epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003103 (compound organ)
0009569 (subdivision of trunk)
0004211 (nephron epithelium)
0009773 (renal tubule)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0001231 (nephron tubule)
0004819 (kidney epithelium)
0005173 (abdominal segment element)
0004810 (nephron tubule epithelium)
0001285 (nephron)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0007684 (uriniferous tubule)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000151 (human renal epithelial cell sample)

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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