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FF:11595-120H2: 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 17:11, 29 March 2012


Name:Renal Proximal Tubular Epithelial Cell, donor2
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 numberlot:5110
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-penis-0.0149
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-0.063
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12087

Jaspar motifP-value
MA0002.20.466
MA0003.10.295
MA0004.10.541
MA0006.10.0728
MA0007.10.0806
MA0009.10.278
MA0014.10.43
MA0017.10.00783
MA0018.20.517
MA0019.10.508
MA0024.10.156
MA0025.10.182
MA0027.10.996
MA0028.10.062
MA0029.10.422
MA0030.10.42
MA0031.10.0292
MA0035.20.0651
MA0038.10.105
MA0039.20.0173
MA0040.10.52
MA0041.10.293
MA0042.10.756
MA0043.10.0573
MA0046.14.80796e-20
MA0047.20.612
MA0048.10.486
MA0050.10.02
MA0051.10.215
MA0052.10.0552
MA0055.10.215
MA0057.10.0903
MA0058.10.386
MA0059.10.35
MA0060.15.2846e-4
MA0061.10.428
MA0062.20.00266
MA0065.20.00757
MA0066.10.168
MA0067.10.114
MA0068.10.369
MA0069.10.352
MA0070.10.164
MA0071.10.0604
MA0072.10.793
MA0073.10.985
MA0074.10.613
MA0076.10.00196
MA0077.10.723
MA0078.10.756
MA0079.20.581
MA0080.20.00295
MA0081.10.0905
MA0083.10.712
MA0084.10.00163
MA0087.10.444
MA0088.10.773
MA0090.10.00305
MA0091.10.831
MA0092.10.562
MA0093.10.53
MA0099.22.55505e-8
MA0100.10.135
MA0101.10.505
MA0102.20.0348
MA0103.17.56379e-8
MA0104.20.825
MA0105.10.998
MA0106.10.117
MA0107.10.275
MA0108.28.30472e-7
MA0111.10.472
MA0112.20.0356
MA0113.10.813
MA0114.10.0319
MA0115.10.101
MA0116.10.535
MA0117.10.146
MA0119.10.612
MA0122.10.175
MA0124.10.834
MA0125.10.293
MA0131.10.0737
MA0135.10.219
MA0136.19.94843e-4
MA0137.20.0683
MA0138.20.537
MA0139.10.393
MA0140.10.267
MA0141.10.00721
MA0142.10.712
MA0143.10.511
MA0144.10.684
MA0145.10.0593
MA0146.10.122
MA0147.10.975
MA0148.10.739
MA0149.10.0547
MA0150.10.483
MA0152.10.222
MA0153.11.2713e-8
MA0154.10.194
MA0155.10.132
MA0156.10.00921
MA0157.10.0863
MA0159.10.0251
MA0160.10.0481
MA0162.10.111
MA0163.10.908
MA0164.10.89
MA0258.10.192
MA0259.10.363



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: CNhs12087

Novel motifP-value
10.801
100.484
1000.477
1010.0169
1020.476
1030.352
1040.539
1050.109
1060.0169
1070.0252
1080.347
1090.0541
110.175
1100.388
1110.954
1120.971
1130.167
1140.605
1150.669
1160.812
1170.687
1180.342
1190.195
120.59
1200.546
1210.777
1220.0741
1230.134
1240.218
1250.917
1260.478
1270.154
1280.189
1290.0212
130.19
1300.521
1310.173
1320.119
1330.0994
1340.239
1350.502
1360.289
1370.142
1380.621
1390.881
140.444
1400.793
1410.817
1420.469
1430.74
1440.712
1450.359
1460.0347
1470.272
1480.296
1490.164
150.476
1500.292
1510.406
1520.0565
1530.675
1540.329
1550.827
1560.0558
1570.187
1580.832
1590.98
160.154
1600.123
1610.599
1620.0574
1630.295
1640.692
1650.491
1660.664
1670.45
1680.505
1690.133
170.345
180.273
190.446
20.134
200.895
210.445
220.245
230.0985
240.974
250.971
260.134
270.234
280.701
290.857
30.832
300.08
310.462
320.924
330.142
340.427
350.259
360.952
370.544
380.192
390.162
40.0761
400.00418
410.641
420.831
430.448
440.28
450.201
460.484
470.74
480.387
490.66
50.815
500.272
510.557
520.259
530.725
540.457
550.632
560.316
570.402
580.84
590.06
60.13
600.182
610.553
620.912
630.173
640.192
650.0536
660.2
670.899
680.742
690.0504
70.475
700.98
710.917
720.846
730.0765
740.291
750.974
760.114
770.00869
780.478
790.941
80.25
800.224
810.566
820.986
830.488
840.812
850.499
860.808
870.0369
880.604
890.103
90.615
900.0764
910.835
920.56
930.726
940.946
950.169
960.555
970.843
980.511
990.00724



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: CNhs12087


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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