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FF:11254-116F3: 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 16:37, 29 March 2012


Name:Prostate Stromal Cells, donor1
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 stage55 years old adult
sexmale
age55
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-penis-0.0269
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-lymphoma0.369
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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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: CNhs10883

Jaspar motifP-value
MA0002.20.111
MA0003.10.68
MA0004.10.133
MA0006.10.442
MA0007.10.808
MA0009.10.794
MA0014.10.233
MA0017.10.863
MA0018.22.71662e-5
MA0019.10.461
MA0024.10.0299
MA0025.10.0329
MA0027.10.4
MA0028.10.0636
MA0029.10.764
MA0030.10.354
MA0031.10.113
MA0035.20.897
MA0038.10.156
MA0039.20.0768
MA0040.10.112
MA0041.10.516
MA0042.10.577
MA0043.10.0103
MA0046.10.444
MA0047.20.495
MA0048.10.0205
MA0050.10.285
MA0051.10.0911
MA0052.10.175
MA0055.10.407
MA0057.10.121
MA0058.10.0267
MA0059.10.924
MA0060.10.694
MA0061.10.19
MA0062.20.334
MA0065.20.656
MA0066.10.993
MA0067.10.0103
MA0068.10.373
MA0069.10.206
MA0070.10.946
MA0071.10.529
MA0072.10.406
MA0073.10.769
MA0074.10.483
MA0076.10.156
MA0077.10.397
MA0078.10.832
MA0079.20.0937
MA0080.26.79852e-9
MA0081.10.0356
MA0083.10.1
MA0084.10.269
MA0087.10.508
MA0088.10.0848
MA0090.10.0113
MA0091.19.2341e-4
MA0092.10.418
MA0093.10.174
MA0099.20.28
MA0100.10.282
MA0101.10.00933
MA0102.20.535
MA0103.10.00122
MA0104.20.28
MA0105.10.479
MA0106.10.225
MA0107.10.00686
MA0108.20.0133
MA0111.10.783
MA0112.20.00816
MA0113.10.409
MA0114.10.686
MA0115.10.645
MA0116.10.149
MA0117.10.734
MA0119.10.155
MA0122.10.295
MA0124.10.942
MA0125.10.236
MA0131.10.927
MA0135.10.358
MA0136.17.20599e-9
MA0137.20.562
MA0138.20.441
MA0139.10.665
MA0140.10.724
MA0141.10.82
MA0142.10.0804
MA0143.10.663
MA0144.10.887
MA0145.10.437
MA0146.10.851
MA0147.10.653
MA0148.10.819
MA0149.10.95
MA0150.10.327
MA0152.10.157
MA0153.10.566
MA0154.10.859
MA0155.10.366
MA0156.18.81267e-5
MA0157.10.242
MA0159.10.492
MA0160.10.352
MA0162.10.0762
MA0163.13.77054e-4
MA0164.10.88
MA0258.10.883
MA0259.10.931



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: CNhs10883

Novel motifP-value
10.991
100.403
1000.0246
1010.113
1020.0214
1030.456
1040.662
1050.275
1060.343
1070.13
1080.799
1090.247
110.901
1100.176
1110.346
1120.716
1130.316
1140.719
1150.0968
1160.166
1170.764
1180.802
1190.056
120.141
1200.378
1210.568
1220.0926
1230.0043
1240.695
1250.453
1260.717
1270.371
1280.52
1290.0273
130.0742
1300.147
1310.693
1320.762
1330.687
1340.429
1350.922
1360.0166
1370.0902
1380.177
1390.286
140.075
1400.201
1410.167
1420.976
1430.877
1440.752
1450.443
1460.794
1470.23
1480.676
1490.355
150.226
1500.337
1510.89
1520.039
1530.668
1540.295
1550.00418
1560.864
1570.15
1580.00499
1590.407
160.157
1600.576
1610.828
1620.809
1630.594
1640.176
1650.855
1660.0742
1670.41
1680.96
1690.0504
170.96
180.219
190.0147
20.374
200.341
210.182
220.711
230.344
240.737
250.365
260.613
270.921
280.0981
290.391
30.919
300.557
310.911
322.39001e-10
330.698
340.861
350.682
360.443
370.284
380.182
390.384
40.0414
400.767
410.0667
420.813
430.894
440.181
450.308
460.825
470.781
480.958
490.183
50.495
500.46
510.705
520.686
530.119
540.723
550.528
560.892
570.644
580.297
590.423
60.985
600.536
610.6
620.578
630.413
640.456
650.64
660.571
670.73
680.835
690.548
70.477
700.145
710.125
720.604
730.0186
740.292
750.657
760.57
770.19
780.129
790.0648
80.108
800.735
810.577
820.164
830.593
840.822
850.164
860.567
870.049
880.332
890.232
90.657
900.188
910.715
920.364
930.618
940.348
950.191
960.305
970.708
980.0362
994.90824e-4



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: CNhs10883


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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