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FF:11404-118D9: 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 17:06, 29 March 2012


Name:Prostate Epithelial Cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueprostate
dev stageNA
sexmale
ageNA
cell typeepithelial cell
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.258
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-0.459
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
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C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
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: CNhs12014

Jaspar motifP-value
MA0002.20.00435
MA0003.10.58
MA0004.10.896
MA0006.10.0647
MA0007.10.833
MA0009.10.156
MA0014.10.196
MA0017.10.624
MA0018.20.0349
MA0019.10.965
MA0024.12.06762e-5
MA0025.10.675
MA0027.10.882
MA0028.10.0338
MA0029.10.783
MA0030.10.613
MA0031.10.234
MA0035.20.675
MA0038.14.54669e-4
MA0039.20.00676
MA0040.10.166
MA0041.10.844
MA0042.10.135
MA0043.10.788
MA0046.10.511
MA0047.20.156
MA0048.10.661
MA0050.12.43501e-13
MA0051.15.07681e-8
MA0052.15.37494e-4
MA0055.10.56
MA0057.10.0532
MA0058.10.939
MA0059.10.814
MA0060.16.80211e-10
MA0061.10.00341
MA0062.20.666
MA0065.20.306
MA0066.10.779
MA0067.10.242
MA0068.10.00158
MA0069.10.0364
MA0070.10.875
MA0071.10.692
MA0072.10.374
MA0073.10.609
MA0074.10.483
MA0076.10.243
MA0077.10.884
MA0078.10.716
MA0079.20.41
MA0080.28.45261e-9
MA0081.10.00465
MA0083.17.41346e-4
MA0084.10.0411
MA0087.10.141
MA0088.10.794
MA0090.10.0143
MA0091.10.114
MA0092.10.481
MA0093.10.992
MA0099.20.748
MA0100.10.0201
MA0101.18.31049e-5
MA0102.20.912
MA0103.12.90013e-11
MA0104.20.942
MA0105.10.0146
MA0106.19.91252e-10
MA0107.15.5015e-5
MA0108.20.00148
MA0111.10.537
MA0112.20.991
MA0113.10.393
MA0114.10.542
MA0115.10.81
MA0116.10.981
MA0117.10.96
MA0119.10.679
MA0122.10.274
MA0124.10.242
MA0125.10.284
MA0131.10.915
MA0135.10.522
MA0136.18.67369e-7
MA0137.20.00141
MA0138.20.701
MA0139.10.499
MA0140.10.0989
MA0141.10.751
MA0142.10.697
MA0143.10.678
MA0144.10.329
MA0145.10.0107
MA0146.10.107
MA0147.10.94
MA0148.10.0336
MA0149.10.166
MA0150.10.781
MA0152.10.595
MA0153.10.987
MA0154.10.291
MA0155.10.378
MA0156.11.21425e-4
MA0157.10.0831
MA0159.10.0977
MA0160.10.894
MA0162.10.394
MA0163.10.0351
MA0164.10.67
MA0258.10.581
MA0259.10.952



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: CNhs12014

Novel motifP-value
10.339
100.722
1000.644
1010.531
1020.213
1030.593
1040.873
1050.656
1060.218
1070.197
1080.0328
1090.0066
110.708
1100.254
1110.0885
1120.162
1130.488
1140.521
1150.0465
1160.912
1170.187
1180.81
1190.249
120.865
1200.00829
1210.167
1220.782
1230.817
1240.0399
1250.725
1260.41
1270.33
1280.96
1290.115
130.129
1300.0257
1310.852
1320.191
1339.63718e-4
1340.0801
1350.5
1360.0198
1370.653
1380.404
1390.027
140.861
1400.0916
1410.459
1420.469
1430.193
1440.18
1450.635
1460.319
1470.662
1480.261
1490.684
150.96
1500.665
1510.482
1520.0365
1530.331
1540.461
1550.637
1560.623
1570.461
1580.912
1590.855
160.0499
1600.443
1610.342
1620.476
1630.786
1640.0154
1650.733
1660.51
1670.682
1680.91
1690.103
170.326
180.179
190.934
20.109
200.312
210.0752
220.7
230.362
240.22
250.603
260.516
270.856
280.615
290.293
30.39
300.382
310.774
320.391
330.586
340.168
350.27
360.249
370.219
380.418
390.46
40.549
400.21
410.142
420.983
430.796
440.107
450.439
460.603
470.379
480.429
490.657
50.457
500.666
510.979
520.562
530.449
540.496
550.355
560.41
570.211
580.939
590.532
60.298
600.601
610.239
620.573
630.172
640.627
650.367
660.551
670.416
680.136
690.174
70.808
700.0039
710.932
720.447
730.0133
740.0736
750.338
760.567
770.0683
780.0107
790.763
80.67
800.0342
810.876
820.356
830.284
840.474
850.46
860.783
870.123
880.702
890.0841
90.24
900.859
910.511
920.377
930.685
940.885
950.0523
960.249
970.246
980.872
990.319



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: CNhs12014


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)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002231 (epithelial cell of prostate)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001046 (hindgut)
0001062 (anatomical entity)
0001353 (anal region)
0001555 (digestive tract)
0002050 (embryonic structure)
0002367 (prostate gland)
0002530 (gland)
0002532 (epiblast (generic))
0003064 (intermediate mesoderm)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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