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FF:10026-101D8: 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 16:27, 29 March 2012


Name:testis, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetestis
dev stage34,53,86 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -17
catalog numberCat:AM6000 Lot:0910061 -17
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-caudate0.761
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-0.062
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs10632

Jaspar motifP-value
MA0002.20.00752
MA0003.10.477
MA0004.10.854
MA0006.10.997
MA0007.10.575
MA0009.10.505
MA0014.10.919
MA0017.10.534
MA0018.21.62795e-4
MA0019.10.00382
MA0024.10.126
MA0025.10.725
MA0027.10.742
MA0028.10.382
MA0029.10.0534
MA0030.10.409
MA0031.10.131
MA0035.20.0212
MA0038.10.012
MA0039.20.0598
MA0040.10.98
MA0041.10.135
MA0042.10.586
MA0043.10.0351
MA0046.10.628
MA0047.20.379
MA0048.10.474
MA0050.10.0812
MA0051.10.0768
MA0052.10.632
MA0055.10.702
MA0057.10.807
MA0058.10.835
MA0059.10.152
MA0060.11.96204e-31
MA0061.18.95055e-5
MA0062.20.239
MA0065.20.834
MA0066.10.533
MA0067.10.543
MA0068.10.508
MA0069.10.882
MA0070.10.161
MA0071.10.471
MA0072.10.237
MA0073.10.988
MA0074.10.615
MA0076.10.139
MA0077.10.314
MA0078.10.139
MA0079.20.059
MA0080.22.85544e-4
MA0081.10.238
MA0083.10.00548
MA0084.10.989
MA0087.10.528
MA0088.10.23
MA0090.10.751
MA0091.10.473
MA0092.10.185
MA0093.10.897
MA0099.26.36805e-9
MA0100.19.66777e-9
MA0101.10.00774
MA0102.20.388
MA0103.10.558
MA0104.20.958
MA0105.12.02201e-11
MA0106.10.00133
MA0107.12.51372e-4
MA0108.28.58621e-5
MA0111.10.422
MA0112.27.32621e-4
MA0113.10.615
MA0114.10.407
MA0115.10.415
MA0116.13.33506e-4
MA0117.10.586
MA0119.10.00615
MA0122.10.936
MA0124.10.775
MA0125.10.899
MA0131.10.221
MA0135.10.0803
MA0136.10.055
MA0137.20.901
MA0138.20.6
MA0139.10.325
MA0140.13.3183e-4
MA0141.10.768
MA0142.10.156
MA0143.10.507
MA0144.10.15
MA0145.10.383
MA0146.10.976
MA0147.10.733
MA0148.10.355
MA0149.10.0549
MA0150.10.00127
MA0152.10.595
MA0153.10.447
MA0154.11.95384e-4
MA0155.10.713
MA0156.10.217
MA0157.10.16
MA0159.10.365
MA0160.10.648
MA0162.10.49
MA0163.10.0037
MA0164.10.934
MA0258.10.0472
MA0259.10.7



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: CNhs10632

Novel motifP-value
10.0343
100.135
1000.935
1010.646
1020.706
1030.627
1040.75
1050.482
1061.04513e-4
1070.0456
1080.289
1090.724
110.101
1100.218
1110.389
1120.0178
1130.606
1140.12
1150.755
1160.461
1170.82
1180.148
1190.105
120.744
1200.148
1210.488
1220.776
1230.00773
1240.212
1250.652
1260.449
1270.463
1280.0221
1290.557
130.4
1300.0534
1310.493
1320.653
1330.617
1340.661
1350.365
1360.0139
1370.281
1380.0873
1390.253
140.334
1400.0284
1410.152
1420.866
1430.821
1440.772
1450.161
1460.88
1470.606
1480.177
1490.259
150.341
1500.413
1510.169
1520.205
1530.4
1540.0742
1550.642
1560.535
1570.898
1580.515
1590.601
160.37
1600.0265
1610.88
1620.82
1630.211
1649.53702e-5
1650.572
1660.708
1670.179
1680.469
1690.116
170.1
180.11
190.699
20.436
200.763
210.413
220.735
230.0398
240.559
250.911
260.127
270.269
280.71
290.61
30.0496
300.48
310.293
320.483
330.865
340.961
350.21
360.0249
370.0829
380.385
390.879
40.0718
400.471
410.252
420.248
430.227
440.415
450.642
460.0432
470.245
480.235
490.802
50.311
500.976
510.206
520.432
530.188
540.296
550.169
560.208
570.0651
580.346
590.219
60.602
600.1
610.749
620.163
630.114
640.35
650.158
666.10982e-9
670.556
680.417
690.86
70.513
700.167
710.0865
720.653
730.19
740.377
750.12
760.241
770.211
780.0571
790.504
80.305
800.915
810.26
820.251
830.848
840.456
850.0632
860.523
870.0739
880.831
890.292
90.92
900.079
910.134
920.118
930.221
940.013
950.878
960.424
970.55
980.347
990.518



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: CNhs10632


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

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000079 (male reproductive system)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000473 (testis)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003101 (male organism)
0003133 (reproductive organ)
0003135 (male reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0007023 (adult organism)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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