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FF:11405-118E1: 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 17:07, 29 March 2012


Name:Prostate Stromal 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 stage40 years old adult
sexmale
age40
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-penis0.0713
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-0.33
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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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: CNhs12015

Jaspar motifP-value
MA0002.20.0325
MA0003.10.376
MA0004.10.409
MA0006.10.11
MA0007.10.671
MA0009.10.579
MA0014.10.316
MA0017.10.708
MA0018.28.99477e-7
MA0019.10.865
MA0024.11.80592e-5
MA0025.10.00816
MA0027.10.46
MA0028.10.00481
MA0029.10.79
MA0030.10.309
MA0031.10.201
MA0035.20.264
MA0038.10.0201
MA0039.20.0164
MA0040.10.128
MA0041.10.513
MA0042.10.535
MA0043.10.00217
MA0046.10.401
MA0047.20.212
MA0048.10.341
MA0050.10.743
MA0051.10.467
MA0052.10.0402
MA0055.10.587
MA0057.10.118
MA0058.10.296
MA0059.10.314
MA0060.11.41646e-12
MA0061.10.401
MA0062.22.7026e-8
MA0065.20.954
MA0066.10.591
MA0067.10.0237
MA0068.10.507
MA0069.10.0654
MA0070.10.775
MA0071.10.438
MA0072.10.467
MA0073.10.784
MA0074.10.0236
MA0076.10.0011
MA0077.10.362
MA0078.10.824
MA0079.20.34
MA0080.21.89086e-9
MA0081.10.00291
MA0083.10.0423
MA0084.10.369
MA0087.10.36
MA0088.10.826
MA0090.10.0111
MA0091.10.00132
MA0092.10.875
MA0093.10.366
MA0099.25.14826e-6
MA0100.10.039
MA0101.10.0402
MA0102.20.832
MA0103.10.073
MA0104.20.0235
MA0105.10.538
MA0106.10.0468
MA0107.10.0573
MA0108.20.894
MA0111.10.321
MA0112.20.0873
MA0113.10.735
MA0114.10.833
MA0115.10.16
MA0116.10.393
MA0117.10.185
MA0119.10.472
MA0122.10.227
MA0124.10.185
MA0125.10.64
MA0131.10.162
MA0135.10.373
MA0136.19.54426e-15
MA0137.20.342
MA0138.20.446
MA0139.10.821
MA0140.10.282
MA0141.10.544
MA0142.10.0217
MA0143.10.314
MA0144.10.967
MA0145.10.412
MA0146.10.0996
MA0147.10.0179
MA0148.10.28
MA0149.10.257
MA0150.10.0202
MA0152.10.454
MA0153.10.128
MA0154.10.942
MA0155.10.0668
MA0156.18.89612e-12
MA0157.10.323
MA0159.10.98
MA0160.10.476
MA0162.10.17
MA0163.10.192
MA0164.10.559
MA0258.10.562
MA0259.10.0895



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: CNhs12015

Novel motifP-value
10.35
100.464
1000.294
1010.496
1020.274
1030.772
1040.841
1050.151
1060.409
1070.0655
1080.0804
1090.795
110.928
1100.687
1110.643
1120.457
1130.661
1140.673
1150.00543
1160.0788
1170.697
1180.675
1190.56
120.44
1200.19
1210.249
1220.0227
1230.0214
1240.396
1250.784
1260.909
1270.859
1280.238
1290.189
130.493
1300.909
1310.274
1320.133
1330.453
1340.432
1350.625
1360.162
1370.0985
1380.39
1390.544
140.364
1400.99
1410.12
1420.645
1430.925
1440.206
1450.826
1460.691
1470.337
1480.534
1490.0657
150.22
1500.402
1510.505
1520.00774
1530.307
1540.0985
1550.0175
1560.476
1570.92
1580.0248
1590.613
160.136
1600.873
1610.798
1620.215
1630.796
1640.0502
1650.414
1660.0458
1670.388
1680.845
1690.0693
170.862
180.576
190.0153
20.136
200.48
210.32
220.155
230.563
240.579
250.0557
260.805
270.49
280.0894
290.568
30.862
300.468
310.391
326.72895e-12
330.518
340.574
350.723
360.0257
370.0922
380.315
390.403
40.151
400.614
410.0789
420.268
430.73
440.0441
450.727
460.815
470.6
480.368
490.242
50.395
500.524
510.634
520.573
530.217
540.57
550.168
560.762
570.42
580.147
590.162
60.633
600.745
610.693
620.399
630.43
640.482
650.551
660.0927
670.78
680.818
690.448
70.0592
700.796
710.996
720.569
730.00895
740.331
750.872
760.999
770.0961
780.189
791.93619e-4
80.314
800.149
810.807
820.272
830.0416
840.726
850.186
860.427
870.108
880.488
890.132
90.812
900.478
910.85
920.644
930.193
940.979
950.3
960.473
970.862
980.313
990.00617



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: CNhs12015


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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