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FF:11515-119H3: 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 Proximal Tubular Epithelial Cell, 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, 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:5127
catalog numberSC4105
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-0.102
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-lymphoma0.127
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: CNhs11330

Jaspar motifP-value
MA0002.21
MA0003.10.391
MA0004.10.524
MA0006.10.0456
MA0007.10.0484
MA0009.10.306
MA0014.10.229
MA0017.10.0164
MA0018.20.189
MA0019.10.64
MA0024.10.0605
MA0025.10.613
MA0027.10.158
MA0028.10.446
MA0029.10.273
MA0030.10.455
MA0031.10.0411
MA0035.20.0727
MA0038.10.00242
MA0039.20.00755
MA0040.10.813
MA0041.10.283
MA0042.10.957
MA0043.10.238
MA0046.11.83958e-31
MA0047.20.309
MA0048.10.528
MA0050.10.128
MA0051.10.909
MA0052.10.329
MA0055.10.0433
MA0057.10.08
MA0058.10.52
MA0059.10.497
MA0060.14.51853e-10
MA0061.10.853
MA0062.20.0709
MA0065.20.0478
MA0066.10.652
MA0067.10.0186
MA0068.10.721
MA0069.10.154
MA0070.10.0529
MA0071.10.451
MA0072.10.675
MA0073.10.99
MA0074.10.777
MA0076.10.0519
MA0077.10.271
MA0078.10.451
MA0079.20.532
MA0080.20.0148
MA0081.10.117
MA0083.10.411
MA0084.10.00418
MA0087.10.482
MA0088.10.894
MA0090.12.42803e-4
MA0091.10.0521
MA0092.10.91
MA0093.10.503
MA0099.22.8437e-10
MA0100.10.524
MA0101.10.163
MA0102.20.0128
MA0103.12.07991e-8
MA0104.20.844
MA0105.10.35
MA0106.10.098
MA0107.10.155
MA0108.22.32413e-5
MA0111.10.439
MA0112.20.464
MA0113.10.795
MA0114.10.0368
MA0115.10.0554
MA0116.10.524
MA0117.10.0785
MA0119.10.932
MA0122.10.275
MA0124.10.36
MA0125.10.214
MA0131.10.32
MA0135.10.265
MA0136.10.111
MA0137.20.527
MA0138.20.754
MA0139.10.585
MA0140.10.759
MA0141.10.184
MA0142.10.488
MA0143.10.296
MA0144.10.432
MA0145.10.0888
MA0146.10.243
MA0147.10.98
MA0148.10.764
MA0149.10.0301
MA0150.10.898
MA0152.10.124
MA0153.14.15736e-18
MA0154.10.824
MA0155.10.373
MA0156.10.14
MA0157.10.0706
MA0159.10.128
MA0160.10.078
MA0162.10.159
MA0163.10.224
MA0164.10.649
MA0258.10.72
MA0259.10.526



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: CNhs11330

Novel motifP-value
10.528
100.122
1000.285
1010.00869
1020.321
1030.732
1040.88
1050.0996
1060.169
1070.0144
1080.666
1090.0556
110.518
1100.541
1110.972
1120.508
1130.115
1140.0579
1150.584
1160.463
1170.359
1180.562
1190.493
120.825
1200.187
1210.34
1220.0179
1230.0468
1240.156
1250.244
1260.4
1270.352
1280.439
1290.0372
130.152
1300.322
1310.0751
1320.204
1330.0185
1340.55
1350.327
1360.076
1370.283
1380.209
1390.102
140.388
1400.468
1410.541
1420.805
1430.569
1440.316
1450.485
1460.0211
1470.428
1480.31
1490.833
150.846
1500.257
1510.69
1520.057
1530.52
1540.284
1550.881
1560.0216
1570.955
1580.303
1590.516
160.245
1600.171
1610.705
1620.138
1630.495
1640.3
1650.441
1660.537
1670.315
1680.812
1690.288
170.422
180.958
190.972
20.267
200.932
210.337
220.419
230.38
240.455
250.866
260.309
270.292
280.92
290.76
30.367
300.0286
310.663
320.0457
330.0374
340.565
350.00706
360.904
370.736
380.394
390.242
40.17
400.0081
410.288
420.765
430.697
440.595
450.208
460.962
470.697
480.436
490.661
50.53
500.173
510.807
520.276
530.573
540.657
550.377
560.203
570.884
580.674
590.241
60.154
600.291
610.586
620.414
630.194
640.393
650.334
660.0331
670.657
680.588
690.443
70.406
700.0846
710.38
720.841
730.0785
740.198
750.615
760.0861
770.00637
780.642
790.0189
80.522
800.418
810.144
820.0873
830.982
840.649
850.28
860.458
870.0195
880.972
890.162
90.81
900.261
910.417
920.683
930.58
940.443
950.333
960.695
970.83
980.974
996.99081e-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: CNhs11330


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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