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FF:11456-119A7: Difference between revisions

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|creation_date=2011-06-15T12:34:29Z
|creation_date=2011-06-15T12:34:29Z
|def="A fibroblast from cardiac tissue." [GOC:tfm]
|def="A fibroblast from cardiac tissue." [GOC:tfm]
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:09, 29 March 2012


Name:Fibroblast - Cardiac, donor5
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
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 number2832
catalog numberSC6305
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-0.0929
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-lymphoma0.0923
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12057

Jaspar motifP-value
MA0002.20.00266
MA0003.10.773
MA0004.10.348
MA0006.10.154
MA0007.10.397
MA0009.10.704
MA0014.10.887
MA0017.10.0666
MA0018.20.0288
MA0019.10.865
MA0024.10.885
MA0025.10.0496
MA0027.10.55
MA0028.10.00473
MA0029.10.0576
MA0030.10.547
MA0031.10.99
MA0035.20.85
MA0038.10.763
MA0039.20.851
MA0040.10.523
MA0041.10.33
MA0042.10.744
MA0043.10.0262
MA0046.10.0141
MA0047.20.111
MA0048.10.0826
MA0050.10.00895
MA0051.10.189
MA0052.10.0119
MA0055.10.0197
MA0057.10.463
MA0058.10.135
MA0059.10.166
MA0060.10.609
MA0061.10.0364
MA0062.20.425
MA0065.26.72034e-4
MA0066.10.565
MA0067.10.139
MA0068.10.0447
MA0069.10.973
MA0070.10.927
MA0071.10.819
MA0072.10.428
MA0073.10.818
MA0074.10.264
MA0076.10.0821
MA0077.10.119
MA0078.10.234
MA0079.20.304
MA0080.25.97106e-6
MA0081.10.427
MA0083.10.787
MA0084.10.00386
MA0087.10.151
MA0088.10.776
MA0090.10.137
MA0091.10.835
MA0092.10.476
MA0093.10.328
MA0099.20.0554
MA0100.10.713
MA0101.10.885
MA0102.20.953
MA0103.12.2864e-4
MA0104.20.0432
MA0105.10.00255
MA0106.10.86
MA0107.10.615
MA0108.20.439
MA0111.10.361
MA0112.20.0304
MA0113.10.126
MA0114.10.00524
MA0115.10.144
MA0116.10.00701
MA0117.10.184
MA0119.10.88
MA0122.10.78
MA0124.10.54
MA0125.10.484
MA0131.10.359
MA0135.10.0457
MA0136.16.26749e-5
MA0137.20.481
MA0138.20.304
MA0139.10.147
MA0140.10.676
MA0141.10.498
MA0142.10.0483
MA0143.10.292
MA0144.10.618
MA0145.10.568
MA0146.10.683
MA0147.10.0767
MA0148.10.297
MA0149.10.257
MA0150.10.0822
MA0152.10.0967
MA0153.10.207
MA0154.10.0445
MA0155.10.854
MA0156.10.447
MA0157.10.375
MA0159.10.323
MA0160.10.044
MA0162.10.278
MA0163.10.0592
MA0164.10.553
MA0258.10.0684
MA0259.10.201



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: CNhs12057

Novel motifP-value
10.179
100.378
1000.976
1010.118
1020.457
1030.345
1040.792
1050.27
1060.354
1070.877
1080.755
1090.65
110.55
1100.499
1110.038
1120.319
1130.0574
1140.121
1150.481
1160.442
1170.984
1180.533
1190.358
120.223
1200.116
1210.82
1220.0274
1230.00447
1240.00525
1250.601
1260.659
1270.071
1280.7
1290.204
130.446
1300.545
1310.93
1320.201
1330.391
1340.475
1350.605
1360.151
1370.17
1380.806
1390.382
140.199
1400.704
1410.528
1420.0592
1430.543
1440.861
1450.464
1460.901
1470.52
1480.226
1490.157
150.0667
1500.35
1510.652
1520.0735
1530.738
1540.835
1550.00265
1560.446
1570.306
1580.0082
1590.2
160.895
1600.369
1610.422
1620.997
1630.391
1640.298
1650.0673
1660.498
1670.266
1680.647
1690.87
170.512
180.632
190.774
20.884
200.627
210.617
220.682
230.676
240.466
250.0659
260.926
270.766
280.278
290.751
30.728
300.977
310.94
323.34248e-4
330.801
340.71
350.0828
360.145
370.999
380.333
390.514
40.0158
400.0648
410.339
420.396
430.137
440.832
450.395
460.253
470.443
480.999
490.0666
50.255
500.557
510.354
520.451
530.172
540.602
550.673
560.426
570.659
580.0403
590.533
60.62
600.172
610.564
620.0761
630.607
640.417
650.674
660.924
670.951
680.834
690.725
70.129
700.0478
710.231
720.491
730.0352
740.756
750.409
760.924
770.682
780.532
790.147
80.883
800.19
810.103
820.0287
830.391
840.731
850.474
860.972
870.0119
880.956
890.436
90.729
900.331
910.419
920.517
930.208
940.0596
950.134
960.12
970.513
980.0153
990.0643



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: CNhs12057


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)
0002494 (cardiocyte)
0002548 (cardiac fibroblast)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)

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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