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FF:11253-116F2: 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 Epithelial Cells (polarized), 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 stage56 years old adult
sexmale
age56
cell typeepithelial cell
cell lineNA
companyCell systems
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-penis0.0124
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-lymphoma0.429
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: CNhs10882

Jaspar motifP-value
MA0002.28.13508e-4
MA0003.10.96
MA0004.10.0122
MA0006.10.535
MA0007.10.711
MA0009.10.128
MA0014.10.0239
MA0017.12.07906e-12
MA0018.20.866
MA0019.10.405
MA0024.11.1328e-5
MA0025.10.0783
MA0027.10.649
MA0028.10.00131
MA0029.10.0132
MA0030.10.147
MA0031.10.105
MA0035.26.51313e-4
MA0038.10.00336
MA0039.20.0126
MA0040.10.143
MA0041.10.544
MA0042.10.392
MA0043.10.785
MA0046.15.61761e-72
MA0047.25.23731e-5
MA0048.10.8
MA0050.15.27617e-4
MA0051.10.0551
MA0052.10.0218
MA0055.10.0164
MA0057.10.79
MA0058.19.25277e-4
MA0059.10.0205
MA0060.11.46278e-12
MA0061.17.69277e-5
MA0062.20.015
MA0065.24.58583e-4
MA0066.10.397
MA0067.10.0478
MA0068.10.64
MA0069.10.797
MA0070.10.194
MA0071.10.621
MA0072.10.466
MA0073.10.564
MA0074.10.232
MA0076.10.00121
MA0077.10.215
MA0078.10.29
MA0079.20.4
MA0080.21.43322e-11
MA0081.10.0174
MA0083.10.0506
MA0084.10.544
MA0087.10.733
MA0088.10.86
MA0090.10.0561
MA0091.10.0473
MA0092.10.0769
MA0093.10.00662
MA0099.21.80387e-7
MA0100.10.566
MA0101.10.0188
MA0102.20.679
MA0103.12.97776e-7
MA0104.20.00509
MA0105.15.15989e-6
MA0106.10.225
MA0107.10.00243
MA0108.20.143
MA0111.10.654
MA0112.20.16
MA0113.10.689
MA0114.11.06626e-16
MA0115.11.71884e-6
MA0116.12.19497e-4
MA0117.10.681
MA0119.10.00171
MA0122.10.401
MA0124.10.331
MA0125.10.016
MA0131.10.421
MA0135.10.197
MA0136.11.64551e-7
MA0137.20.101
MA0138.20.616
MA0139.10.267
MA0140.10.0271
MA0141.10.109
MA0142.10.833
MA0143.10.845
MA0144.10.0817
MA0145.10.257
MA0146.10.403
MA0147.10.032
MA0148.11.70039e-4
MA0149.10.558
MA0150.15.73255e-4
MA0152.10.337
MA0153.11.49207e-53
MA0154.10.00317
MA0155.10.75
MA0156.11.02017e-4
MA0157.10.976
MA0159.10.666
MA0160.10.258
MA0162.10.645
MA0163.10.139
MA0164.10.112
MA0258.10.616
MA0259.10.357



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: CNhs10882

Novel motifP-value
10.357
100.3
1000.249
1010.448
1020.606
1030.726
1040.673
1050.782
1060.0982
1070.523
1080.935
1090.431
110.261
1100.328
1110.841
1120.0957
1130.0361
1140.296
1150.627
1160.66
1170.636
1180.333
1190.88
120.931
1200.247
1210.501
1220.7
1230.0708
1240.871
1250.0128
1260.543
1270.3
1280.022
1290.88
130.0354
1300.591
1310.058
1320.872
1330.147
1340.0858
1350.0666
1360.0114
1370.00993
1380.0265
1390.0799
140.243
1400.992
1410.996
1420.736
1430.0113
1440.369
1450.168
1460.518
1470.789
1480.435
1490.963
150.339
1500.31
1510.656
1520.141
1530.136
1540.0624
1550.0573
1560.581
1570.873
1580.806
1590.532
160.554
1600.14
1610.641
1620.878
1630.224
1640.934
1650.604
1660.0723
1670.87
1680.506
1690.462
170.729
180.0204
190.32
20.535
200.396
210.421
220.665
230.0195
240.827
250.782
260.794
270.489
280.711
290.504
30.302
300.682
310.796
320.154
330.908
340.442
350.249
360.893
370.597
380.954
390.415
40.784
400.0967
410.0134
420.413
430.14
440.184
450.62
460.434
470.944
480.796
490.197
50.21
500.623
510.985
520.711
530.332
540.994
550.207
560.872
570.343
580.457
590.246
60.492
600.263
610.22
620.233
630.409
640.643
650.148
660.0234
670.167
680.343
690.275
70.458
700.176
710.296
720.356
730.26
740.0392
750.518
760.747
770.928
780.0053
790.304
80.508
800.483
810.144
820.024
830.511
840.347
850.0687
860.358
870.216
880.894
890.358
90.0464
900.478
910.00673
920.102
930.702
940.0318
950.148
960.0297
970.904
980.468
990.487



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: CNhs10882


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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