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FF:11452-119A3: 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 17:00, 29 March 2012


Name:Fibroblast - Cardiac, donor4
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 number2136
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-0.169
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-lymphoma0.197
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: CNhs11909

Jaspar motifP-value
MA0002.27.33094e-4
MA0003.10.159
MA0004.10.52
MA0006.10.756
MA0007.10.449
MA0009.10.191
MA0014.10.525
MA0017.10.0545
MA0018.20.156
MA0019.10.504
MA0024.10.15
MA0025.10.00443
MA0027.10.667
MA0028.10.732
MA0029.10.196
MA0030.10.569
MA0031.10.15
MA0035.20.298
MA0038.10.0683
MA0039.20.84
MA0040.10.299
MA0041.10.13
MA0042.10.209
MA0043.10.135
MA0046.10.559
MA0047.20.443
MA0048.10.773
MA0050.10.761
MA0051.10.499
MA0052.10.515
MA0055.10.666
MA0057.10.655
MA0058.10.592
MA0059.10.0556
MA0060.10.0115
MA0061.15.12828e-4
MA0062.20.315
MA0065.26.98969e-4
MA0066.10.0736
MA0067.10.529
MA0068.10.00579
MA0069.10.969
MA0070.10.735
MA0071.10.121
MA0072.10.673
MA0073.10.761
MA0074.10.594
MA0076.10.481
MA0077.10.678
MA0078.10.451
MA0079.20.339
MA0080.26.8228e-4
MA0081.10.354
MA0083.10.144
MA0084.10.182
MA0087.10.256
MA0088.10.497
MA0090.10.0328
MA0091.10.542
MA0092.10.745
MA0093.10.641
MA0099.20.135
MA0100.10.742
MA0101.10.0479
MA0102.20.572
MA0103.14.30793e-5
MA0104.20.127
MA0105.15.40366e-8
MA0106.10.14
MA0107.10.0142
MA0108.20.00258
MA0111.10.509
MA0112.25.3793e-4
MA0113.10.298
MA0114.10.0209
MA0115.10.113
MA0116.11.09335e-4
MA0117.10.737
MA0119.10.516
MA0122.10.826
MA0124.10.378
MA0125.10.271
MA0131.10.595
MA0135.10.367
MA0136.10.00485
MA0137.21.66443e-4
MA0138.20.0798
MA0139.10.0225
MA0140.10.238
MA0141.10.0707
MA0142.10.288
MA0143.10.984
MA0144.10.299
MA0145.10.509
MA0146.10.113
MA0147.10.063
MA0148.10.421
MA0149.10.049
MA0150.10.0948
MA0152.10.0487
MA0153.10.0208
MA0154.10.00206
MA0155.10.423
MA0156.10.156
MA0157.10.59
MA0159.10.0552
MA0160.10.131
MA0162.10.228
MA0163.13.606e-6
MA0164.10.389
MA0258.10.00152
MA0259.10.445



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: CNhs11909

Novel motifP-value
10.0282
100.0719
1000.203
1010.608
1020.221
1030.543
1040.975
1050.984
1060.028
1070.548
1080.205
1090.0156
110.0453
1100.126
1110.00874
1120.123
1130.494
1140.0435
1150.311
1160.35
1170.0623
1180.0886
1190.0452
120.902
1200.199
1210.723
1220.43
1234.96534e-4
1240.247
1250.0104
1260.256
1270.0441
1280.562
1290.39
130.105
1300.0131
1310.147
1320.962
1330.308
1340.462
1350.771
1360.934
1370.753
1380.148
1390.0129
140.601
1400.546
1410.671
1420.619
1430.0236
1440.736
1450.286
1460.696
1470.933
1480.168
1490.705
150.17
1500.372
1510.373
1520.331
1530.459
1540.772
1550.00707
1560.515
1570.632
1580.043
1590.541
160.289
1600.123
1610.293
1620.829
1630.848
1640.121
1650.816
1660.37
1670.0655
1680.453
1690.049
170.212
180.13
190.642
20.92
200.518
210.359
220.781
230.431
240.735
250.245
260.076
270.514
280.586
290.048
30.266
300.561
310.697
320.535
330.514
340.954
350.113
360.00967
370.0779
380.271
390.811
40.0777
400.0137
410.554
420.524
430.155
440.086
450.927
460.0565
470.0699
480.133
490.0944
50.734
500.793
510.51
520.874
530.513
540.663
550.777
560.565
570.218
580.155
590.111
60.478
600.15
610.252
620.0705
630.309
640.0897
650.185
660.835
670.134
680.992
690.133
70.316
700.00871
710.0744
720.897
730.244
740.546
750.0563
760.349
770.137
780.273
790.386
80.124
800.972
810.378
820.0636
830.556
840.563
850.124
860.722
870.981
880.926
890.308
90.973
900.512
910.707
920.389
930.367
940.0354
950.0142
960.239
970.401
980.0944
990.547



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: CNhs11909


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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