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FF:11597-120H4: 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 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
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-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
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-0.0764
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: CNhs12088

Jaspar motifP-value
MA0002.20.178
MA0003.10.375
MA0004.10.626
MA0006.10.151
MA0007.10.0133
MA0009.10.54
MA0014.10.976
MA0017.10.011
MA0018.20.186
MA0019.10.201
MA0024.10.75
MA0025.10.93
MA0027.10.515
MA0028.10.00252
MA0029.10.149
MA0030.10.308
MA0031.10.0369
MA0035.20.0166
MA0038.10.0662
MA0039.20.191
MA0040.10.85
MA0041.10.232
MA0042.10.833
MA0043.10.00615
MA0046.11.22636e-15
MA0047.20.791
MA0048.10.776
MA0050.12.47472e-4
MA0051.10.0132
MA0052.10.357
MA0055.10.181
MA0057.10.163
MA0058.10.922
MA0059.10.445
MA0060.10.0074
MA0061.10.212
MA0062.21.15303e-6
MA0065.20.00644
MA0066.10.208
MA0067.10.00298
MA0068.10.412
MA0069.10.524
MA0070.10.0876
MA0071.10.239
MA0072.10.942
MA0073.10.952
MA0074.10.279
MA0076.17.6063e-6
MA0077.10.121
MA0078.10.227
MA0079.20.844
MA0080.20.00301
MA0081.10.0577
MA0083.10.0224
MA0084.10.00721
MA0087.10.539
MA0088.10.779
MA0090.10.0285
MA0091.10.513
MA0092.10.626
MA0093.10.774
MA0099.21.84398e-6
MA0100.10.209
MA0101.10.32
MA0102.20.00498
MA0103.17.68108e-5
MA0104.20.839
MA0105.10.407
MA0106.10.00705
MA0107.10.268
MA0108.22.74667e-6
MA0111.10.566
MA0112.20.0418
MA0113.10.927
MA0114.10.0232
MA0115.10.388
MA0116.10.241
MA0117.10.211
MA0119.10.369
MA0122.10.799
MA0124.10.445
MA0125.10.73
MA0131.10.0531
MA0135.10.0722
MA0136.11.2055e-4
MA0137.20.182
MA0138.20.418
MA0139.10.531
MA0140.10.232
MA0141.10.0994
MA0142.10.0976
MA0143.10.764
MA0144.10.975
MA0145.10.195
MA0146.10.119
MA0147.10.899
MA0148.10.263
MA0149.10.128
MA0150.10.514
MA0152.10.234
MA0153.18.19573e-9
MA0154.10.107
MA0155.10.0373
MA0156.10.00176
MA0157.10.233
MA0159.10.0542
MA0160.10.13
MA0162.10.0571
MA0163.10.605
MA0164.10.809
MA0258.10.0403
MA0259.10.644



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: CNhs12088

Novel motifP-value
10.876
100.327
1000.417
1010.272
1020.675
1030.577
1040.53
1050.0229
1060.0307
1070.00217
1080.578
1090.319
110.168
1100.294
1110.949
1120.605
1130.429
1140.749
1150.665
1160.306
1170.864
1180.793
1190.37
120.303
1200.29
1210.704
1220.216
1230.415
1240.733
1250.827
1260.603
1270.159
1280.164
1290.00212
130.391
1300.278
1310.354
1320.122
1330.0791
1340.942
1350.775
1360.984
1370.269
1380.289
1390.568
140.551
1400.335
1410.526
1420.197
1430.171
1440.695
1450.255
1460.0719
1470.321
1480.907
1490.125
150.393
1500.352
1510.573
1520.136
1530.0855
1540.254
1550.573
1560.226
1570.267
1580.971
1590.76
160.242
1600.00205
1611
1620.181
1630.931
1640.621
1650.866
1660.974
1670.46
1680.899
1690.0997
170.199
180.289
190.34
20.318
200.691
210.605
220.193
230.192
240.839
250.873
260.0813
270.169
280.371
290.688
30.792
300.142
310.403
320.925
330.0878
340.335
350.841
360.539
370.39
380.392
390.199
40.0556
400.00252
410.997
420.874
430.462
440.847
450.177
460.235
470.553
480.263
490.427
50.725
500.439
510.346
520.341
530.672
540.415
550.983
560.256
570.158
580.97
590.0217
60.324
600.304
610.397
620.943
630.198
640.139
650.0558
660.268
670.617
680.633
690.0574
70.765
700.363
710.777
720.765
730.129
740.402
750.899
760.206
770.0323
780.708
790.829
80.0549
800.977
810.706
820.816
830.716
840.488
850.707
860.696
870.179
880.5
890.139
90.513
900.243
910.0724
920.909
930.895
940.448
950.415
960.572
970.969
980.136
990.0109



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: CNhs12088


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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