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FF:10021-101D3: 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:placenta, 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
tissueplacenta
dev stageadult
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 -12
catalog numberCat:AM6000 Lot:0910061 -12
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-0.111
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-0.118
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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: CNhs10627

Jaspar motifP-value
MA0002.20.103
MA0003.10.0463
MA0004.10.158
MA0006.10.0799
MA0007.10.9
MA0009.10.797
MA0014.10.675
MA0017.10.839
MA0018.20.269
MA0019.10.214
MA0024.10.179
MA0025.10.257
MA0027.10.491
MA0028.18.68178e-5
MA0029.10.195
MA0030.16.53818e-4
MA0031.19.59269e-10
MA0035.27.86351e-4
MA0038.10.339
MA0039.20.0274
MA0040.10.0659
MA0041.10.413
MA0042.10.51
MA0043.10.218
MA0046.10.0643
MA0047.21.96705e-4
MA0048.10.00624
MA0050.10.0856
MA0051.10.307
MA0052.10.838
MA0055.10.06
MA0057.10.938
MA0058.10.122
MA0059.10.00377
MA0060.10.0197
MA0061.10.00149
MA0062.25.39611e-5
MA0065.20.5
MA0066.10.919
MA0067.10.0297
MA0068.10.00958
MA0069.10.637
MA0070.10.396
MA0071.10.998
MA0072.10.719
MA0073.10.67
MA0074.10.445
MA0076.14.86298e-4
MA0077.10.372
MA0078.10.056
MA0079.20.101
MA0080.20.423
MA0081.10.408
MA0083.10.0368
MA0084.10.685
MA0087.10.3
MA0088.10.0594
MA0090.11.40107e-4
MA0091.10.371
MA0092.10.24
MA0093.10.124
MA0099.20.00783
MA0100.10.376
MA0101.10.0116
MA0102.20.739
MA0103.10.195
MA0104.22.39877e-4
MA0105.10.00193
MA0106.10.903
MA0107.10.00952
MA0108.21.90046e-17
MA0111.10.603
MA0112.20.226
MA0113.10.0989
MA0114.10.969
MA0115.10.667
MA0116.10.124
MA0117.10.366
MA0119.10.569
MA0122.10.523
MA0124.10.257
MA0125.10.189
MA0131.10.286
MA0135.10.838
MA0136.10.533
MA0137.20.0189
MA0138.20.443
MA0139.10.418
MA0140.10.00724
MA0141.10.435
MA0142.10.59
MA0143.10.241
MA0144.10.00527
MA0145.10.00113
MA0146.10.55
MA0147.11.38483e-4
MA0148.10.00256
MA0149.10.0556
MA0150.10.0958
MA0152.10.791
MA0153.10.427
MA0154.10.401
MA0155.10.334
MA0156.10.415
MA0157.10.00499
MA0159.10.642
MA0160.10.726
MA0162.10.862
MA0163.10.00713
MA0164.10.293
MA0258.10.931
MA0259.10.136



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: CNhs10627

Novel motifP-value
10.211
100.0846
1000.132
1010.738
1020.465
1030.383
1040.576
1050.33
1060.384
1070.0352
1080.79
1090.382
110.585
1100.562
1110.0044
1120.753
1130.00131
1140.799
1150.779
1160.329
1170.154
1180.327
1190.632
120.217
1200.992
1210.664
1220.836
1230.00968
1240.423
1250.493
1260.255
1270.0318
1280.762
1290.658
130.597
1300.898
1310.203
1320.162
1330.135
1340.469
1350.0278
1360.908
1370.605
1380.6
1390.664
140.711
1400.483
1410.705
1420.483
1430.028
1440.0752
1450.801
1460.123
1470.883
1480.775
1490.175
150.177
1500.783
1510.716
1520.0442
1530.437
1540.315
1550.952
1560.52
1570.294
1580.323
1590.532
160.654
1600.997
1610.302
1620.202
1630.741
1640.113
1650.479
1660.592
1670.00163
1680.897
1690.304
170.713
180.0516
190.139
20.0879
200.122
210.766
220.32
230.0948
240.969
250.56
260.705
270.771
280.945
290.0243
30.43
300.0227
310.885
320.291
330.298
340.152
350.416
360.0978
370.645
380.887
390.388
40.143
400.675
410.119
420.424
430.599
440.918
450.0183
460.433
470.317
480.603
490.47
50.803
500.427
510.834
520.249
530.884
540.765
550.987
560.7
570.456
580.716
590.582
60.545
600.607
610.264
620.722
630.892
640.767
650.5
660.177
670.906
680.331
690.44
70.987
700.972
710.246
720.98
730.785
740.0938
750.0456
760.0503
770.0746
780.931
790.592
80.224
800.353
810.0732
820.986
830.535
840.309
850.44
860.682
870.0476
880.709
890.205
90.181
900.692
910.452
920.972
930.758
940.193
950.115
960.412
970.0857
980.767
990.497



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: CNhs10627


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)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000158 (membranous layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000478 (extraembryonic structure)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0001987 (placenta)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003100 (female organism)
0003124 (chorion)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0004340 (allantois)
0004872 (splanchnic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005631 (extraembryonic membrane)
0005795 (embryonic uterus)
0007023 (adult organism)

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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