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FF:11596-120H3: 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 17:24, 29 March 2012


Name:Renal Cortical Epithelial Cells, 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, renal cortex
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2264
catalog numberSC4115
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-0.147
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-lymphoma0.264
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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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: CNhs12728

Jaspar motifP-value
MA0002.20.0576
MA0003.10.805
MA0004.10.106
MA0006.10.0228
MA0007.10.473
MA0009.10.0887
MA0014.10.157
MA0017.10.491
MA0018.20.978
MA0019.10.256
MA0024.10.0203
MA0025.10.915
MA0027.10.455
MA0028.10.918
MA0029.10.834
MA0030.10.947
MA0031.10.125
MA0035.20.924
MA0038.10.00291
MA0039.20.00363
MA0040.10.801
MA0041.10.607
MA0042.10.52
MA0043.10.525
MA0046.13.44311e-19
MA0047.20.293
MA0048.10.278
MA0050.15.75334e-6
MA0051.10.0136
MA0052.10.688
MA0055.10.208
MA0057.10.255
MA0058.10.0508
MA0059.10.156
MA0060.11.06645e-5
MA0061.10.562
MA0062.20.0225
MA0065.20.687
MA0066.10.714
MA0067.10.0973
MA0068.10.592
MA0069.10.34
MA0070.10.131
MA0071.10.651
MA0072.10.766
MA0073.10.914
MA0074.10.949
MA0076.10.154
MA0077.10.0606
MA0078.10.832
MA0079.20.604
MA0080.24.40449e-6
MA0081.10.01
MA0083.10.739
MA0084.10.156
MA0087.10.806
MA0088.10.578
MA0090.11.4704e-4
MA0091.10.00614
MA0092.10.341
MA0093.10.153
MA0099.28.43974e-5
MA0100.10.605
MA0101.10.94
MA0102.20.0449
MA0103.11.10088e-7
MA0104.20.0293
MA0105.10.121
MA0106.10.0594
MA0107.11
MA0108.20.00755
MA0111.10.333
MA0112.20.53
MA0113.10.231
MA0114.10.882
MA0115.10.652
MA0116.10.0955
MA0117.10.281
MA0119.10.0929
MA0122.10.446
MA0124.10.259
MA0125.10.0475
MA0131.10.527
MA0135.10.556
MA0136.10.00113
MA0137.20.71
MA0138.20.134
MA0139.10.752
MA0140.10.428
MA0141.10.24
MA0142.10.709
MA0143.10.696
MA0144.10.629
MA0145.10.0544
MA0146.10.946
MA0147.10.047
MA0148.10.433
MA0149.10.183
MA0150.10.374
MA0152.10.558
MA0153.11.44742e-14
MA0154.10.365
MA0155.10.826
MA0156.10.0166
MA0157.10.148
MA0159.10.425
MA0160.10.175
MA0162.10.228
MA0163.10.0237
MA0164.10.719
MA0258.10.066
MA0259.10.44



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: CNhs12728

Novel motifP-value
10.203
100.0375
1000.969
1010.0971
1020.318
1030.994
1040.986
1050.558
1060.654
1070.155
1080.503
1090.615
110.399
1100.376
1110.529
1120.419
1130.882
1140.00547
1150.389
1160.262
1170.0752
1180.991
1190.857
120.314
1200.104
1210.803
1220.273
1230.00446
1240.0322
1250.689
1260.361
1270.413
1280.66
1290.0646
130.884
1300.395
1310.136
1320.238
1330.148
1340.211
1350.0746
1360.0982
1370.076
1380.174
1390.00109
140.674
1400.252
1410.687
1420.214
1430.138
1440.274
1450.55
1460.346
1470.574
1480.0189
1490.739
150.626
1500.992
1510.847
1520.036
1530.864
1540.315
1550.326
1560.453
1570.898
1580.519
1590.989
160.743
1600.958
1610.904
1620.544
1630.137
1640.472
1650.538
1660.748
1670.359
1680.622
1690.867
170.864
180.448
190.247
20.754
200.837
210.773
220.889
230.57
240.39
250.707
260.34
270.583
280.903
290.898
30.198
300.0259
310.962
320.0128
330.0971
340.793
358.12367e-4
360.477
370.949
380.836
390.308
40.983
400.0777
410.133
420.29
430.213
440.244
450.226
460.348
470.583
480.587
490.0217
50.108
500.269
510.937
520.615
530.181
540.792
550.0617
560.295
570.544
580.229
590.915
60.253
600.774
610.284
620.0639
630.642
640.45
650.932
660.0891
670.695
680.0287
690.298
70.564
700.0381
710.0611
720.833
730.125
740.078
750.476
760.0868
770.0575
780.307
790.323
80.349
800.151
810.0247
820.0711
830.0193
840.761
850.0535
860.24
870.167
880.878
890.38
90.496
900.83
910.339
920.555
930.326
940.173
950.0245
960.43
970.888
980.0363
990.00796



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: CNhs12728


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)
0002584 (renal cortical 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)
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)
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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