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FF:11517-119H5: 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 16:45, 29 March 2012


Name:Renal Epithelial Cells, donor1
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 numberNA
catalog numberSC4125
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
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-0.0806
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-lymphoma0.0475
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11332

Jaspar motifP-value
MA0002.20.514
MA0003.10.41
MA0004.10.231
MA0006.10.137
MA0007.10.131
MA0009.11
MA0014.10.664
MA0017.10.396
MA0018.20.15
MA0019.10.0341
MA0024.10.0133
MA0025.10.0424
MA0027.10.443
MA0028.10.494
MA0029.10.441
MA0030.10.868
MA0031.10.268
MA0035.20.134
MA0038.14.41426e-4
MA0039.20.0221
MA0040.10.597
MA0041.10.181
MA0042.10.599
MA0043.10.931
MA0046.11.68027e-14
MA0047.20.506
MA0048.10.69
MA0050.10.0012
MA0051.10.0925
MA0052.10.0877
MA0055.10.00357
MA0057.10.492
MA0058.10.281
MA0059.10.869
MA0060.15.80189e-14
MA0061.10.623
MA0062.20.261
MA0065.20.825
MA0066.10.681
MA0067.10.13
MA0068.10.993
MA0069.10.654
MA0070.14.95692e-4
MA0071.10.682
MA0072.10.748
MA0073.10.948
MA0074.10.648
MA0076.10.215
MA0077.10.024
MA0078.10.715
MA0079.20.244
MA0080.26.50161e-4
MA0081.10.119
MA0083.10.00296
MA0084.10.306
MA0087.10.828
MA0088.10.962
MA0090.10.00582
MA0091.10.361
MA0092.10.38
MA0093.10.228
MA0099.20.0142
MA0100.10.249
MA0101.10.698
MA0102.20.0253
MA0103.10.00463
MA0104.20.518
MA0105.10.0744
MA0106.10.158
MA0107.10.563
MA0108.24.20113e-10
MA0111.10.0598
MA0112.20.761
MA0113.10.676
MA0114.10.883
MA0115.10.689
MA0116.10.131
MA0117.10.4
MA0119.10.0948
MA0122.10.942
MA0124.10.679
MA0125.10.332
MA0131.10.496
MA0135.10.123
MA0136.10.00479
MA0137.20.854
MA0138.20.887
MA0139.10.845
MA0140.10.724
MA0141.10.705
MA0142.10.63
MA0143.10.206
MA0144.10.731
MA0145.10.283
MA0146.10.0668
MA0147.10.495
MA0148.10.507
MA0149.10.575
MA0150.10.453
MA0152.10.0673
MA0153.11.81872e-7
MA0154.10.73
MA0155.10.158
MA0156.10.138
MA0157.10.16
MA0159.10.851
MA0160.10.731
MA0162.10.293
MA0163.10.127
MA0164.10.965
MA0258.10.395
MA0259.10.376



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: CNhs11332

Novel motifP-value
10.0543
100.0073
1000.473
1010.0411
1020.478
1030.177
1040.489
1050.182
1060.864
1070.334
1080.731
1090.727
110.731
1100.833
1110.21
1120.212
1130.0737
1140.0105
1150.918
1160.697
1170.24
1180.859
1190.622
120.478
1200.744
1210.467
1220.212
1230.00227
1240.211
1250.195
1260.929
1270.238
1280.589
1290.263
130.897
1300.0398
1310.187
1320.147
1330.142
1340.78
1350.321
1360.153
1370.0643
1380.0362
1390.0122
140.566
1400.227
1410.076
1420.708
1430.404
1440.705
1450.768
1460.0987
1470.748
1480.0128
1490.686
150.189
1500.474
1510.749
1520.107
1530.0456
1540.109
1550.897
1560.504
1570.548
1580.255
1590.611
160.465
1600.383
1610.572
1620.461
1630.597
1640.129
1650.122
1660.76
1670.0482
1680.33
1690.445
170.918
180.326
190.731
20.51
200.977
210.337
220.378
230.593
240.917
250.343
260.541
270.69
280.243
290.312
30.0657
300.0528
310.61
320.341
330.279
340.408
350.0275
360.674
370.824
380.918
390.694
40.525
400.0357
410.409
420.234
430.184
440.507
450.309
460.396
470.551
480.986
490.111
50.143
500.317
510.871
520.714
530.149
540.957
550.0574
560.652
570.308
580.0767
590.237
60.228
600.631
610.766
620.0116
630.869
640.968
650.384
660.141
670.541
680.312
690.166
70.471
700.0798
710.0872
720.328
730.108
740.186
750.142
760.0637
770.406
780.489
790.207
80.844
800.495
810.025
820.0635
830.787
840.426
850.142
860.411
870.0986
880.81
890.847
90.734
900.00106
910.54
920.0408
930.633
940.0793
950.961
960.198
970.927
980.387
990.0221



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: CNhs11332


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

UBERON: Anatomy
0000025 (tube)
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000080 (mesonephros)
0000083 (mesonephric tubule)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001008 (renal system)
0001062 (anatomical entity)
0001231 (nephron tubule)
0001285 (nephron)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003060 (pronephric duct)
0003064 (intermediate mesoderm)
0003074 (mesonephric duct)
0003081 (lateral plate mesoderm)
0003103 (compound organ)
0003104 (mesenchyme)
0003220 (metanephric mesenchyme)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003914 (epithelial tube)
0003918 (kidney mesenchyme)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004211 (nephron epithelium)
0004810 (nephron tubule epithelium)
0004819 (kidney epithelium)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005103 (mesonephric epithelium)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0006553 (renal duct)
0006554 (urinary system structure)
0006555 (excretory tube)
0007684 (uriniferous tubule)
0007687 (kidney field)
0009142 (entire embryonic mesenchyme)
0009201 (nephric duct)

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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