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FF:10057-101H3: 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 16:52, 29 March 2012


Name:umbilical cord, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueumbilical cord
dev stage31 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB110269
catalog numberCat:RtHFN: Umbilical cor
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.445
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-0.137
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11765

Jaspar motifP-value
MA0002.20.0679
MA0003.10.0389
MA0004.10.0225
MA0006.10.211
MA0007.10.321
MA0009.10.185
MA0014.10.705
MA0017.10.419
MA0018.20.0563
MA0019.10.657
MA0024.10.0294
MA0025.10.0496
MA0027.10.426
MA0028.11.26767e-10
MA0029.10.575
MA0030.10.895
MA0031.10.747
MA0035.20.435
MA0038.10.634
MA0039.20.233
MA0040.10.981
MA0041.10.588
MA0042.10.319
MA0043.10.00336
MA0046.10.628
MA0047.20.297
MA0048.10.0531
MA0050.10.0019
MA0051.19.59935e-4
MA0052.18.2051e-11
MA0055.10.0429
MA0057.10.418
MA0058.14.69515e-4
MA0059.10.0351
MA0060.14.52904e-4
MA0061.10.0683
MA0062.25.61428e-21
MA0065.20.289
MA0066.10.523
MA0067.10.0732
MA0068.10.785
MA0069.10.0971
MA0070.10.526
MA0071.10.146
MA0072.10.716
MA0073.10.426
MA0074.10.589
MA0076.11.85537e-14
MA0077.10.926
MA0078.10.74
MA0079.20.381
MA0080.27.14818e-7
MA0081.12.9546e-4
MA0083.18.37088e-10
MA0084.10.0558
MA0087.10.536
MA0088.10.0418
MA0090.12.17177e-4
MA0091.10.00129
MA0092.10.0886
MA0093.10.00577
MA0099.25.47245e-8
MA0100.10.154
MA0101.10.0141
MA0102.20.173
MA0103.10.202
MA0104.29.57607e-4
MA0105.10.568
MA0106.10.885
MA0107.10.0132
MA0108.23.29143e-34
MA0111.10.328
MA0112.21.42648e-4
MA0113.10.00237
MA0114.10.765
MA0115.10.129
MA0116.10.76
MA0117.10.38
MA0119.10.116
MA0122.10.189
MA0124.10.58
MA0125.10.413
MA0131.10.181
MA0135.10.908
MA0136.12.37799e-16
MA0137.20.527
MA0138.20.0075
MA0139.10.49
MA0140.10.999
MA0141.10.124
MA0142.10.0349
MA0143.10.471
MA0144.10.563
MA0145.10.0348
MA0146.10.616
MA0147.10.0038
MA0148.10.0537
MA0149.10.148
MA0150.10.00332
MA0152.10.0732
MA0153.10.348
MA0154.10.136
MA0155.10.0385
MA0156.14.5628e-16
MA0157.10.37
MA0159.10.662
MA0160.10.591
MA0162.10.0853
MA0163.10.65
MA0164.10.983
MA0258.10.00183
MA0259.10.127



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: CNhs11765

Novel motifP-value
10.892
100.312
1000.842
1010.876
1020.77
1030.879
1040.787
1050.836
1060.0272
1070.00283
1080.134
1090.618
110.714
1100.606
1110.861
1120.49
1131.57509e-4
1140.544
1150.411
1160.257
1170.0537
1180.494
1190.151
120.13
1200.562
1210.655
1220.0648
1230.207
1240.742
1250.921
1260.423
1270.882
1280.0752
1290.487
130.539
1300.907
1310.211
1320.069
1330.545
1340.613
1350.194
1360.262
1370.362
1380.632
1390.139
140.974
1400.531
1410.687
1420.428
1430.501
1440.217
1450.789
1460.679
1470.0388
1480.589
1490.0251
150.372
1500.825
1510.104
1520.329
1530.425
1540.67
1550.652
1560.899
1570.399
1580.65
1590.501
160.165
1600.0498
1610.53
1620.143
1630.678
1640.82
1650.307
1660.0805
1670.108
1680.0832
1690.022
170.327
180.847
190.00947
20.0238
200.0679
210.699
220.242
230.0137
240.453
250.655
260.904
270.318
280.766
290.148
30.671
300.038
310.468
321.99363e-9
330.233
340.233
350.67
360.0772
370.993
380.609
390.089
40.814
400.553
410.337
420.713
430.625
440.324
450.131
460.244
470.847
480.882
490.428
50.672
500.816
510.586
520.139
530.782
540.425
550.551
560.996
570.461
580.68
590.175
60.307
600.222
610.767
620.275
630.516
640.483
650.115
660.0563
670.448
680.436
690.247
70.806
700.535
710.753
720.914
730.972
740.2
750.405
760.144
770.0738
780.512
790.16
80.641
800.498
810.478
820.115
830.734
840.425
850.0344
860.518
870.0211
880.485
890.0727
90.477
900.202
910.0095
920.0502
930.736
940.45
950.0301
960.192
970.78
980.515
990.216



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: CNhs11765


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)
0000087 (inner cell mass)
0000091 (bilaminar disc)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000479 (tissue)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002331 (umbilical cord)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0004120 (mesoderm-derived structure)
0005423 (developing anatomical structure)
0005728 (extraembryonic mesoderm)
0007806 (connecting stalk)
0008780 (inner cell mass derived epiblast)

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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