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FF:11332-117E9: 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 Stromal 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 stage24 years old adult
sexmale
age24
cell typeprostatic stromal 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-penis0.171
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-lymphoma0.346
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: CNhs11973

Jaspar motifP-value
MA0002.20.0513
MA0003.10.857
MA0004.10.573
MA0006.10.447
MA0007.10.451
MA0009.10.857
MA0014.10.191
MA0017.10.797
MA0018.22.86681e-7
MA0019.10.134
MA0024.10.257
MA0025.10.00661
MA0027.10.894
MA0028.10.83
MA0029.10.739
MA0030.10.00297
MA0031.10.00819
MA0035.20.174
MA0038.10.52
MA0039.20.0353
MA0040.10.806
MA0041.10.204
MA0042.10.429
MA0043.13.03928e-4
MA0046.10.0383
MA0047.20.049
MA0048.10.0534
MA0050.10.17
MA0051.10.584
MA0052.10.00166
MA0055.10.43
MA0057.10.155
MA0058.10.173
MA0059.10.431
MA0060.10.00597
MA0061.10.786
MA0062.20.001
MA0065.20.258
MA0066.10.377
MA0067.10.00257
MA0068.10.287
MA0069.10.0673
MA0070.10.533
MA0071.10.476
MA0072.10.307
MA0073.10.656
MA0074.10.0823
MA0076.10.263
MA0077.10.322
MA0078.10.468
MA0079.20.126
MA0080.22.01693e-9
MA0081.10.0184
MA0083.10.052
MA0084.10.152
MA0087.10.74
MA0088.10.321
MA0090.10.181
MA0091.10.00584
MA0092.10.626
MA0093.10.48
MA0099.20.0228
MA0100.10.484
MA0101.10.0626
MA0102.20.0404
MA0103.10.0442
MA0104.20.788
MA0105.10.0529
MA0106.10.0498
MA0107.10.0186
MA0108.20.944
MA0111.10.867
MA0112.20.00303
MA0113.10.624
MA0114.10.406
MA0115.10.861
MA0116.10.026
MA0117.10.41
MA0119.10.0111
MA0122.10.138
MA0124.10.121
MA0125.10.666
MA0131.10.776
MA0135.10.0122
MA0136.16.43025e-11
MA0137.20.00357
MA0138.20.751
MA0139.10.663
MA0140.10.406
MA0141.10.338
MA0142.10.216
MA0143.10.782
MA0144.10.237
MA0145.10.803
MA0146.10.218
MA0147.10.713
MA0148.10.0603
MA0149.10.329
MA0150.10.0657
MA0152.10.211
MA0153.10.576
MA0154.10.386
MA0155.10.442
MA0156.15.56816e-10
MA0157.10.037
MA0159.10.87
MA0160.10.283
MA0162.10.243
MA0163.12.94248e-7
MA0164.10.953
MA0258.10.219
MA0259.10.902



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: CNhs11973

Novel motifP-value
10.425
100.0317
1000.0408
1010.481
1020.26
1030.474
1040.47
1050.0294
1060.683
1070.0486
1080.358
1090.143
110.22
1100.0868
1110.747
1120.618
1130.518
1140.849
1150.0093
1160.00275
1170.302
1180.386
1190.967
120.071
1200.0338
1210.304
1220.00792
1230.123
1240.772
1250.18
1260.966
1270.976
1280.773
1290.122
130.248
1300.587
1310.369
1320.525
1330.529
1340.413
1350.256
1360.0816
1370.311
1380.356
1390.884
140.061
1400.563
1410.328
1420.332
1430.651
1440.591
1450.702
1460.124
1470.0663
1480.39
1490.137
150.597
1500.225
1510.935
1520.062
1530.856
1540.566
1550.198
1560.772
1570.166
1580.0233
1590.47
160.0343
1600.418
1610.575
1620.437
1630.885
1640.0735
1650.943
1660.0287
1670.664
1680.185
1690.0127
170.915
180.123
190.00189
20.551
200.745
210.0278
220.525
230.932
240.732
250.437
260.126
270.832
280.156
290.15
30.326
300.87
310.702
324.44196e-11
330.754
340.649
350.675
360.456
370.0228
380.48
390.334
40.137
400.985
410.0264
420.886
430.881
440.00761
450.195
460.239
470.565
480.54
490.569
50.348
500.7
510.845
520.772
530.26
540.762
550.44
560.761
570.746
580.664
590.118
60.226
600.895
610.901
620.776
630.371
640.868
650.624
660.772
670.792
680.694
690.558
70.389
700.929
710.0206
720.434
730.0187
740.0565
750.145
760.786
770.147
780.36
790.00174
80.0185
800.0181
810.704
820.902
830.95
840.975
850.918
860.371
870.124
880.308
890.0887
90.975
900.79
910.839
920.781
930.241
940.388
950.0604
960.588
970.898
980.178
990.00233



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: CNhs11973


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000499 (stromal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002622 (prostate stromal 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)
0002384 (connective tissue)
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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