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FF:11318-117D4: 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 17:03, 29 March 2012


Name:Fibroblast - Gingival, donor2
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 number3540
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-penis0.0485
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-lymphoma0.523
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11961

Jaspar motifP-value
MA0002.20.0218
MA0003.10.426
MA0004.10.506
MA0006.10.862
MA0007.10.347
MA0009.10.718
MA0014.10.276
MA0017.10.115
MA0018.23.5504e-4
MA0019.10.0339
MA0024.11.45693e-7
MA0025.14.84202e-5
MA0027.10.675
MA0028.10.0862
MA0029.10.766
MA0030.10.039
MA0031.10.0108
MA0035.20.0101
MA0038.10.106
MA0039.20.521
MA0040.10.286
MA0041.10.21
MA0042.10.427
MA0043.11.27182e-5
MA0046.10.1
MA0047.20.17
MA0048.11.85358e-5
MA0050.10.00522
MA0051.10.00637
MA0052.10.133
MA0055.15.61985e-4
MA0057.10.28
MA0058.10.181
MA0059.10.944
MA0060.16.80374e-4
MA0061.11.92876e-4
MA0062.20.102
MA0065.20.357
MA0066.10.797
MA0067.10.0041
MA0068.10.41
MA0069.10.399
MA0070.10.988
MA0071.10.835
MA0072.10.385
MA0073.10.283
MA0074.10.671
MA0076.10.631
MA0077.10.939
MA0078.10.954
MA0079.20.0826
MA0080.23.2403e-10
MA0081.10.048
MA0083.10.0878
MA0084.10.0398
MA0087.10.865
MA0088.10.00791
MA0090.10.323
MA0091.10.706
MA0092.10.19
MA0093.10.4
MA0099.20.0163
MA0100.10.144
MA0101.12.88886e-4
MA0102.20.00117
MA0103.10.0344
MA0104.20.965
MA0105.10.274
MA0106.10.327
MA0107.13.59626e-7
MA0108.20.0173
MA0111.10.971
MA0112.20.582
MA0113.10.917
MA0114.10.235
MA0115.10.932
MA0116.10.916
MA0117.10.164
MA0119.10.0754
MA0122.10.19
MA0124.10.658
MA0125.10.532
MA0131.10.472
MA0135.10.131
MA0136.14.61585e-10
MA0137.20.00857
MA0138.20.853
MA0139.10.628
MA0140.10.0659
MA0141.10.679
MA0142.10.338
MA0143.10.365
MA0144.10.0578
MA0145.10.122
MA0146.10.0798
MA0147.10.743
MA0148.10.258
MA0149.10.232
MA0150.10.00845
MA0152.10.0871
MA0153.10.077
MA0154.10.0904
MA0155.10.425
MA0156.13.0224e-7
MA0157.10.00714
MA0159.10.00674
MA0160.10.182
MA0162.10.0141
MA0163.10.106
MA0164.10.609
MA0258.10.876
MA0259.10.516



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: CNhs11961

Novel motifP-value
10.891
100.0477
1000.155
1010.953
1020.668
1030.342
1040.948
1050.329
1060.00622
1070.958
1080.868
1090.38
110.39
1100.0228
1110.598
1120.552
1130.0435
1140.256
1150.0476
1160.15
1170.0733
1180.456
1190.643
120.597
1200.142
1210.728
1220.0139
1230.504
1240.567
1250.531
1260.652
1270.743
1280.593
1290.612
130.863
1300.211
1310.191
1320.565
1330.75
1340.673
1350.00563
1360.159
1370.0703
1380.481
1390.00144
140.188
1400.967
1410.332
1420.542
1430.219
1440.46
1450.247
1460.547
1470.184
1480.595
1490.747
150.421
1500.601
1510.707
1520.312
1530.969
1540.431
1550.204
1560.213
1570.168
1580.0197
1590.297
160.862
1600.0666
1610.716
1620.098
1630.623
1640.219
1650.788
1660.667
1670.99
1680.363
1690.801
170.601
180.774
190.239
20.838
200.431
213.83236e-4
220.723
230.139
240.972
250.347
260.0357
270.69
280.317
290.617
30.559
300.684
310.73
320.0698
330.429
340.275
350.341
360.41
370.349
380.563
390.859
40.0637
400.785
410.019
420.964
430.314
440.305
450.0513
460.779
470.774
480.337
490.294
50.0921
500.354
510.722
520.172
530.659
540.694
550.949
560.985
570.405
580.166
590.986
60.439
600.0653
610.733
620.315
630.537
640.743
650.423
660.315
670.374
680.954
690.48
70.245
700.162
710.902
720.225
730.688
740.237
750.662
760.284
770.803
780.696
790.575
80.196
800.00223
810.858
820.151
830.366
840.676
850.0956
860.147
870.344
880.206
890.336
90.408
900.518
910.673
920.245
930.292
940.783
950.213
960.512
970.633
980.291
993.25337e-4



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: CNhs11961


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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