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FF:11331-117E8: 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 17:04, 29 March 2012


Name:Prostate 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
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-penis0.00591
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-0.268
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: CNhs11972

Jaspar motifP-value
MA0002.20.405
MA0003.10.577
MA0004.10.119
MA0006.10.00542
MA0007.10.709
MA0009.10.323
MA0014.10.642
MA0017.10.615
MA0018.27.34117e-4
MA0019.10.256
MA0024.11.09633e-7
MA0025.10.0803
MA0027.10.507
MA0028.10.272
MA0029.10.199
MA0030.10.289
MA0031.10.225
MA0035.20.166
MA0038.14.93129e-4
MA0039.20.0758
MA0040.10.355
MA0041.10.72
MA0042.10.23
MA0043.10.00544
MA0046.10.88
MA0047.20.361
MA0048.10.761
MA0050.11.9262e-6
MA0051.14.88252e-4
MA0052.10.0213
MA0055.10.894
MA0057.10.0434
MA0058.10.0314
MA0059.10.705
MA0060.13.44309e-7
MA0061.10.238
MA0062.20.0168
MA0065.20.287
MA0066.10.132
MA0067.10.00156
MA0068.10.0743
MA0069.10.0313
MA0070.10.412
MA0071.10.225
MA0072.10.565
MA0073.10.819
MA0074.10.27
MA0076.10.107
MA0077.10.109
MA0078.10.543
MA0079.20.0755
MA0080.21.02942e-6
MA0081.10.0143
MA0083.10.267
MA0084.10.291
MA0087.10.909
MA0088.10.557
MA0090.18.55012e-4
MA0091.10.713
MA0092.10.971
MA0093.10.0685
MA0099.20.369
MA0100.10.0472
MA0101.10.0167
MA0102.20.036
MA0103.12.07342e-6
MA0104.20.0399
MA0105.10.522
MA0106.11.26774e-10
MA0107.10.0146
MA0108.20.368
MA0111.10.92
MA0112.20.0633
MA0113.10.457
MA0114.10.925
MA0115.10.362
MA0116.10.782
MA0117.10.311
MA0119.10.697
MA0122.10.533
MA0124.10.58
MA0125.10.899
MA0131.10.505
MA0135.10.837
MA0136.15.69551e-6
MA0137.20.00279
MA0138.20.894
MA0139.10.257
MA0140.10.066
MA0141.10.47
MA0142.10.95
MA0143.10.177
MA0144.10.377
MA0145.10.0149
MA0146.10.24
MA0147.10.0833
MA0148.10.249
MA0149.10.408
MA0150.10.612
MA0152.10.338
MA0153.10.334
MA0154.10.54
MA0155.10.717
MA0156.13.0597e-4
MA0157.10.059
MA0159.10.172
MA0160.10.249
MA0162.10.0249
MA0163.10.84
MA0164.10.239
MA0258.10.528
MA0259.10.609



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: CNhs11972

Novel motifP-value
10.899
100.213
1000.85
1010.0861
1020.253
1030.173
1040.663
1050.82
1060.037
1070.176
1080.0344
1090.0475
110.613
1100.415
1110.43
1120.202
1130.758
1140.32
1150.0189
1160.42
1170.443
1180.914
1190.826
120.215
1200.00933
1210.824
1220.758
1230.336
1240.151
1250.168
1260.83
1270.62
1280.206
1290.0859
130.469
1300.0559
1310.965
1320.14
1330.107
1340.152
1350.632
1360.0406
1370.03
1380.982
1390.707
140.992
1400.126
1410.95
1420.885
1430.998
1440.549
1450.583
1460.44
1470.549
1480.995
1490.255
150.638
1500.227
1510.276
1520.00355
1530.981
1540.755
1550.802
1560.638
1570.627
1580.0477
1590.75
160.0271
1600.951
1610.821
1620.327
1630.944
1640.479
1650.82
1660.574
1670.214
1680.377
1690.102
170.335
180.7
190.502
20.0243
200.736
210.816
220.592
230.385
240.132
250.536
260.902
270.279
280.823
290.366
30.515
300.172
310.609
320.414
330.383
340.53
350.386
360.0473
370.127
380.764
390.219
40.681
400.421
410.505
420.665
430.863
440.0494
450.223
460.721
470.486
480.366
490.237
50.664
500.619
510.894
520.256
530.168
540.734
550.35
560.736
570.966
580.782
590.104
60.279
600.403
610.987
620.693
630.227
640.906
650.577
660.431
670.525
680.338
690.145
70.864
700.0348
710.863
720.868
730.00175
740.0246
750.478
760.966
770.00552
780.0622
790.105
80.464
800.0802
810.684
820.25
830.0811
840.606
850.146
860.736
870.00754
880.652
890.0215
90.686
900.578
910.367
920.534
930.578
940.303
950.068
960.605
970.634
980.781
990.0397



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: CNhs11972


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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