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FF:10020-101D2: 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 16:26, 29 March 2012


Name:ovary, 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
tissueovary
dev stage47,75,84 years old adult
sexfemale
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 -11
catalog numberCat:AM6000 Lot:0910061 -11
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
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-0.116
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs10626

Jaspar motifP-value
MA0002.20.0144
MA0003.10.502
MA0004.10.185
MA0006.10.914
MA0007.10.286
MA0009.10.127
MA0014.10.293
MA0017.10.308
MA0018.20.388
MA0019.10.0449
MA0024.10.278
MA0025.10.27
MA0027.10.825
MA0028.10.00641
MA0029.10.148
MA0030.10.00133
MA0031.10.0468
MA0035.20.659
MA0038.10.397
MA0039.20.682
MA0040.10.704
MA0041.10.221
MA0042.10.427
MA0043.10.721
MA0046.10.0148
MA0047.20.187
MA0048.10.257
MA0050.10.0208
MA0051.10.103
MA0052.10.0238
MA0055.10.0515
MA0057.10.853
MA0058.10.13
MA0059.10.0119
MA0060.10.535
MA0061.10.00516
MA0062.21.79654e-4
MA0065.20.0172
MA0066.10.0633
MA0067.10.281
MA0068.10.00319
MA0069.10.776
MA0070.10.947
MA0071.10.235
MA0072.10.43
MA0073.10.563
MA0074.10.906
MA0076.10.0316
MA0077.10.832
MA0078.10.154
MA0079.20.32
MA0080.20.0203
MA0081.10.298
MA0083.15.90324e-4
MA0084.10.885
MA0087.10.261
MA0088.10.0366
MA0090.10.128
MA0091.10.639
MA0092.10.817
MA0093.10.225
MA0099.22.5681e-9
MA0100.10.548
MA0101.10.0434
MA0102.20.316
MA0103.10.111
MA0104.20.0233
MA0105.12.35978e-8
MA0106.10.0304
MA0107.10.0631
MA0108.23.46374e-11
MA0111.10.423
MA0112.20.00501
MA0113.10.816
MA0114.10.075
MA0115.10.128
MA0116.14.31331e-4
MA0117.10.412
MA0119.10.174
MA0122.10.705
MA0124.10.285
MA0125.10.503
MA0131.10.588
MA0135.10.181
MA0136.10.00424
MA0137.20.001
MA0138.20.643
MA0139.10.529
MA0140.10.409
MA0141.10.106
MA0142.10.286
MA0143.10.321
MA0144.10.347
MA0145.10.87
MA0146.10.372
MA0147.10.0143
MA0148.10.252
MA0149.10.0137
MA0150.10.00148
MA0152.10.198
MA0153.10.0107
MA0154.10.014
MA0155.10.451
MA0156.10.0241
MA0157.10.566
MA0159.10.123
MA0160.10.167
MA0162.10.16
MA0163.18.65375e-8
MA0164.10.422
MA0258.10.0276
MA0259.10.222



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: CNhs10626

Novel motifP-value
10.0135
100.0222
1000.148
1010.674
1020.405
1030.163
1040.424
1050.303
1060.378
1070.925
1080.633
1090.0333
110.0298
1100.143
1110.00641
1120.719
1130.652
1140.00773
1150.688
1160.651
1170.0183
1180.168
1190.0554
120.657
1200.0596
1210.924
1220.929
1230.00194
1240.492
1250.142
1260.909
1270.261
1280.619
1290.255
130.066
1300.251
1310.136
1320.294
1330.0345
1340.215
1350.183
1360.378
1370.782
1380.303
1390.0623
140.734
1400.212
1410.479
1420.787
1430.00554
1440.829
1450.178
1460.58
1470.769
1480.0234
1490.818
150.0911
1500.358
1510.615
1520.841
1530.719
1540.47
1550.138
1560.869
1570.958
1580.34
1590.667
160.101
1600.629
1610.305
1620.611
1630.832
1640.0869
1650.769
1660.751
1670.0261
1680.805
1690.172
170.224
180.0803
190.907
20.358
200.259
210.142
220.968
230.676
240.677
250.393
260.0172
270.826
280.662
290.0159
30.0831
300.0652
310.725
320.473
330.291
340.367
350.172
360.0179
370.0794
380.332
390.566
40.341
400.0418
410.103
420.274
430.144
440.427
450.485
460.0515
470.0368
480.118
490.072
50.386
500.872
510.552
520.528
530.613
540.713
550.283
560.595
570.0613
580.322
590.771
60.587
600.649
610.473
620.135
630.248
640.14
650.305
660.0983
670.621
680.947
690.311
70.314
700.0173
710.0244
720.751
730.107
740.549
750.014
760.0956
770.796
780.0132
790.852
80.104
800.391
810.36
820.451
830.94
840.606
850.661
860.493
870.0451
880.804
890.64
90.551
900.015
910.557
920.579
930.117
940.0198
950.0154
960.501
970.634
980.0473
990.815



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: CNhs10626


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)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0000992 (female gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female 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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