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FF:11237-116D4: 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 16:35, 29 March 2012


Name:Fibroblast - Gingival, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stagefetus
sexunknown
agefetal
cell typefibroblast
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number428
catalog numberSC2625
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-penis-0.128
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-lymphoma0.0672
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: CNhs10866

Jaspar motifP-value
MA0002.20.327
MA0003.10.73
MA0004.10.515
MA0006.10.703
MA0007.10.0572
MA0009.10.569
MA0014.10.116
MA0017.10.463
MA0018.24.69453e-6
MA0019.10.0351
MA0024.10.0826
MA0025.16.36803e-5
MA0027.10.162
MA0028.10.00139
MA0029.10.613
MA0030.10.431
MA0031.10.724
MA0035.29.75224e-4
MA0038.10.512
MA0039.20.0867
MA0040.10.586
MA0041.10.445
MA0042.10.838
MA0043.18.48901e-4
MA0046.10.546
MA0047.20.364
MA0048.10.0278
MA0050.10.195
MA0051.10.876
MA0052.10.358
MA0055.10.0526
MA0057.10.703
MA0058.10.545
MA0059.10.906
MA0060.10.512
MA0061.10.00124
MA0062.20.641
MA0065.20.179
MA0066.10.762
MA0067.10.00977
MA0068.10.86
MA0069.10.243
MA0070.10.253
MA0071.10.587
MA0072.10.661
MA0073.10.581
MA0074.10.961
MA0076.10.0539
MA0077.10.151
MA0078.10.449
MA0079.20.713
MA0080.22.43619e-9
MA0081.10.404
MA0083.10.985
MA0084.10.0214
MA0087.10.408
MA0088.11.30209e-4
MA0090.10.0328
MA0091.10.683
MA0092.10.919
MA0093.10.599
MA0099.29.32491e-5
MA0100.10.209
MA0101.19.36289e-6
MA0102.20.252
MA0103.11.84525e-5
MA0104.20.699
MA0105.10.209
MA0106.10.00864
MA0107.11.78236e-8
MA0108.29.02415e-4
MA0111.10.169
MA0112.20.715
MA0113.10.0973
MA0114.10.83
MA0115.10.248
MA0116.10.867
MA0117.10.196
MA0119.10.00464
MA0122.10.82
MA0124.10.0435
MA0125.10.34
MA0131.10.279
MA0135.10.267
MA0136.11.12609e-4
MA0137.20.256
MA0138.20.553
MA0139.10.705
MA0140.10.114
MA0141.10.857
MA0142.10.0742
MA0143.10.501
MA0144.10.235
MA0145.10.447
MA0146.10.209
MA0147.10.904
MA0148.10.632
MA0149.10.697
MA0150.10.385
MA0152.10.291
MA0153.10.314
MA0154.10.486
MA0155.10.336
MA0156.10.00471
MA0157.10.884
MA0159.10.00662
MA0160.10.401
MA0162.10.111
MA0163.10.225
MA0164.10.597
MA0258.10.923
MA0259.10.619



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: CNhs10866

Novel motifP-value
10.891
100.197
1000.964
1010.773
1020.362
1030.889
1040.75
1050.79
1060.0564
1070.886
1080.974
1090.636
110.879
1100.0892
1110.643
1120.263
1137.45984e-4
1140.458
1150.47
1160.468
1170.018
1180.927
1190.774
120.44
1200.885
1210.525
1220.0111
1230.86
1240.762
1250.808
1260.436
1270.881
1280.923
1290.498
130.14
1300.124
1310.705
1320.43
1330.887
1340.217
1350.0315
1360.729
1370.194
1380.592
1390.0406
140.366
1400.982
1410.0684
1420.15
1430.402
1440.187
1450.186
1460.189
1470.041
1480.772
1490.707
150.348
1500.785
1510.699
1520.562
1530.031
1540.706
1550.0326
1560.759
1570.222
1581.9784e-4
1590.0497
160.818
1600.967
1610.567
1620.702
1630.612
1640.199
1650.541
1660.98
1670.824
1680.871
1690.0644
170.915
180.852
190.0356
20.69
200.688
210.0277
220.305
230.754
240.47
250.116
260.793
270.44
280.471
290.816
30.308
300.773
310.847
320.0648
330.583
340.309
350.227
360.0932
370.144
380.795
390.603
40.0421
400.0669
410.0887
420.25
430.923
440.034
450.797
460.714
470.439
480.991
490.988
50.738
500.0981
510.896
520.592
530.42
540.714
550.0333
560.985
570.209
580.285
590.731
60.443
600.0661
610.46
620.394
630.139
640.35
650.415
660.395
670.897
680.865
690.628
70.197
700.635
710.798
720.994
730.431
740.0595
750.868
760.25
770.176
780.277
790.373
80.547
800.13
810.776
820.244
830.488
840.344
850.252
860.829
870.0755
880.551
890.611
90.8
900.552
910.808
920.274
930.733
940.147
950.421
960.711
970.714
980.64
992.60464e-5



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: CNhs10866


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002552 (fibroblast of gingiva)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001828 (gingiva)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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