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FF:11676-122H2: 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 17:12, 29 March 2012


Name:Renal Proximal Tubular Epithelial Cell, 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, proximal tubule
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 numberSC4105
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-penis0.107
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-lymphoma0.0954
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 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: CNhs12120

Jaspar motifP-value
MA0002.20.844
MA0003.10.384
MA0004.10.663
MA0006.10.0736
MA0007.10.0295
MA0009.10.651
MA0014.10.871
MA0017.10.112
MA0018.20.272
MA0019.10.524
MA0024.10.155
MA0025.10.89
MA0027.10.23
MA0028.10.0333
MA0029.10.484
MA0030.10.19
MA0031.10.0158
MA0035.20.173
MA0038.10.0193
MA0039.20.0606
MA0040.10.816
MA0041.10.308
MA0042.10.999
MA0043.10.0198
MA0046.15.87274e-24
MA0047.20.13
MA0048.10.417
MA0050.15.06451e-6
MA0051.10.00693
MA0052.10.555
MA0055.10.0217
MA0057.10.257
MA0058.10.993
MA0059.10.682
MA0060.16.89533e-7
MA0061.10.987
MA0062.21.20706e-4
MA0065.20.0499
MA0066.10.369
MA0067.10.00761
MA0068.10.801
MA0069.10.287
MA0070.10.103
MA0071.10.26
MA0072.10.571
MA0073.10.975
MA0074.10.27
MA0076.10.00106
MA0077.10.0424
MA0078.10.599
MA0079.20.648
MA0080.22.40255e-6
MA0081.10.00212
MA0083.10.0657
MA0084.10.0313
MA0087.10.348
MA0088.10.887
MA0090.10.00483
MA0091.10.724
MA0092.10.987
MA0093.10.764
MA0099.26.96642e-6
MA0100.10.139
MA0101.10.95
MA0102.25.57884e-4
MA0103.19.53262e-6
MA0104.20.46
MA0105.10.766
MA0106.10.02
MA0107.10.927
MA0108.23.69271e-4
MA0111.10.402
MA0112.20.245
MA0113.10.743
MA0114.10.185
MA0115.10.536
MA0116.10.779
MA0117.10.0796
MA0119.10.992
MA0122.10.445
MA0124.10.502
MA0125.10.655
MA0131.10.0826
MA0135.10.32
MA0136.11.90112e-7
MA0137.20.0285
MA0138.20.907
MA0139.10.901
MA0140.10.828
MA0141.10.095
MA0142.10.522
MA0143.10.495
MA0144.10.648
MA0145.10.128
MA0146.10.086
MA0147.10.667
MA0148.10.754
MA0149.10.247
MA0150.10.553
MA0152.10.116
MA0153.12.46969e-10
MA0154.10.578
MA0155.10.0753
MA0156.11.87247e-4
MA0157.10.0506
MA0159.10.481
MA0160.10.237
MA0162.10.0653
MA0163.10.479
MA0164.10.904
MA0258.10.301
MA0259.10.131



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: CNhs12120

Novel motifP-value
10.52
100.155
1000.0793
1010.0395
1020.379
1030.325
1040.547
1050.17
1060.0432
1079.93439e-4
1080.338
1090.407
110.48
1100.344
1110.786
1120.301
1130.187
1140.108
1150.334
1160.268
1170.801
1180.517
1190.275
120.873
1200.476
1210.785
1220.407
1230.291
1240.222
1250.294
1260.561
1270.333
1280.298
1290.381
130.25
1300.155
1310.0717
1320.0661
1330.125
1340.623
1350.81
1360.0768
1370.0311
1380.0536
1390.127
140.621
1400.625
1410.345
1420.704
1430.547
1440.793
1450.229
1460.0492
1470.657
1480.126
1490.915
150.544
1500.13
1510.565
1520.0527
1530.095
1540.306
1550.686
1560.463
1570.627
1580.201
1590.756
160.445
1600.0473
1610.58
1620.0393
1630.954
1640.224
1650.0798
1660.97
1670.368
1680.144
1690.203
170.256
180.799
190.699
20.23
200.982
210.698
220.262
230.718
240.869
250.571
260.131
270.306
280.316
290.866
30.479
300.118
310.497
320.927
330.122
340.262
350.172
360.826
370.378
380.546
390.343
40.442
400.00277
410.288
420.485
430.918
440.883
450.154
460.757
470.658
480.34
490.48
50.302
500.213
510.358
520.282
530.494
540.52
550.766
560.189
570.945
580.301
590.0471
60.373
600.47
610.438
620.209
630.303
640.414
650.11
660.117
670.461
680.88
690.0286
70.968
700.461
710.491
720.276
730.0456
740.0953
750.754
760.117
770.0154
780.428
790.81
80.225
800.0996
810.117
820.269
830.876
840.6
850.449
860.54
870.0541
880.621
890.589
90.718
900.0293
910.981
920.437
930.203
940.365
950.361
960.313
970.704
980.705
992.6779e-4



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: CNhs12120


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)
0000075 (columnar/cuboidal epithelial cell)
0000222 (mesodermal cell)
0000239 (brush border epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002306 (epithelial cell of proximal tubule)
0002321 (embryonic cell)
0002371 (somatic cell)
0002518 (kidney epithelial cell)
0002584 (renal cortical epithelial cell)
1000494 (nephron tubule epithelial cell)
1000497 (kidney cell)
1000507 (kidney tubule cell)
1000615 (kidney cortex 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)
0001225 (cortex of kidney)
0001231 (nephron tubule)
0001285 (nephron)
0001851 (cortex)
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)
0004134 (proximal tubule)
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)
0006853 (renal cortex tubule)
0007684 (uriniferous tubule)
0007685 (region of nephron 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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