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FF:11460-119B2: 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, donor6
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 number2151
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-0.0758
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-lymphoma0.372
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: CNhs12061

Jaspar motifP-value
MA0002.20.00137
MA0003.10.509
MA0004.10.273
MA0006.10.237
MA0007.10.461
MA0009.10.569
MA0014.10.605
MA0017.10.0823
MA0018.20.00157
MA0019.10.869
MA0024.16.95738e-5
MA0025.15.42245e-4
MA0027.10.716
MA0028.10.0162
MA0029.10.338
MA0030.10.0927
MA0031.10.263
MA0035.20.858
MA0038.10.334
MA0039.20.576
MA0040.10.622
MA0041.10.857
MA0042.10.929
MA0043.11.3628e-4
MA0046.10.0178
MA0047.20.621
MA0048.10.00885
MA0050.10.00173
MA0051.10.00248
MA0052.10.00943
MA0055.10.00772
MA0057.10.986
MA0058.10.174
MA0059.10.55
MA0060.10.00202
MA0061.17.59442e-6
MA0062.20.65
MA0065.20.00203
MA0066.10.376
MA0067.10.0168
MA0068.10.0742
MA0069.10.984
MA0070.10.827
MA0071.10.896
MA0072.10.36
MA0073.10.733
MA0074.10.849
MA0076.10.117
MA0077.10.556
MA0078.10.771
MA0079.20.624
MA0080.29.85847e-7
MA0081.10.514
MA0083.10.573
MA0084.10.024
MA0087.10.19
MA0088.10.3
MA0090.10.105
MA0091.10.515
MA0092.10.974
MA0093.10.293
MA0099.20.0199
MA0100.10.368
MA0101.10.0181
MA0102.20.139
MA0103.12.79595e-6
MA0104.20.077
MA0105.15.77358e-5
MA0106.10.937
MA0107.12.57612e-4
MA0108.20.653
MA0111.10.955
MA0112.20.0948
MA0113.10.451
MA0114.10.0042
MA0115.10.241
MA0116.10.0409
MA0117.10.0829
MA0119.10.0873
MA0122.10.889
MA0124.10.575
MA0125.10.668
MA0131.10.479
MA0135.10.0236
MA0136.11.62524e-5
MA0137.20.179
MA0138.20.326
MA0139.10.0575
MA0140.10.486
MA0141.10.801
MA0142.10.221
MA0143.10.549
MA0144.10.351
MA0145.10.491
MA0146.10.631
MA0147.10.177
MA0148.10.747
MA0149.10.28
MA0150.10.138
MA0152.10.156
MA0153.10.351
MA0154.10.0259
MA0155.10.687
MA0156.10.2
MA0157.10.0723
MA0159.10.143
MA0160.10.0735
MA0162.10.523
MA0163.10.0771
MA0164.10.85
MA0258.10.0396
MA0259.10.537



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: CNhs12061

Novel motifP-value
10.33
100.714
1000.824
1010.561
1020.451
1030.322
1040.852
1050.0736
1060.241
1070.759
1080.514
1090.508
110.62
1100.137
1110.0725
1120.236
1130.0712
1140.0775
1150.388
1160.408
1170.933
1180.374
1190.372
120.165
1200.183
1210.79
1220.0518
1230.0583
1240.19
1250.0988
1260.276
1270.209
1280.921
1290.39
130.666
1300.0669
1310.998
1320.408
1330.531
1340.534
1350.806
1360.236
1370.13
1380.525
1390.018
140.211
1400.886
1410.959
1420.0495
1430.396
1440.99
1450.561
1460.888
1470.428
1480.192
1490.473
150.178
1500.308
1510.273
1520.823
1530.462
1540.671
1550.00425
1560.916
1570.3
1580.00735
1590.146
160.988
1600.989
1610.633
1620.782
1630.396
1640.863
1650.17
1660.525
1670.182
1680.433
1690.715
170.548
180.187
190.442
20.904
200.753
210.235
220.622
230.289
240.866
250.112
260.444
270.625
280.245
290.436
30.954
300.978
310.512
320.00202
330.931
340.796
350.0903
360.0652
370.544
380.524
390.273
40.0596
400.00893
410.429
420.782
430.126
440.248
450.323
460.542
470.802
480.758
490.0893
50.326
500.497
510.484
520.45
530.281
540.55
550.551
560.457
570.966
580.0725
590.427
60.942
600.0956
610.54
620.12
630.858
640.599
650.37
660.476
670.816
680.465
690.73
70.235
700.0186
710.388
720.553
730.279
740.967
750.276
760.879
770.991
780.673
790.111
80.922
800.266
810.29
820.0362
830.54
840.782
850.1
860.843
870.014
880.58
890.637
90.727
900.605
910.988
920.769
930.566
940.0626
950.637
960.451
970.516
980.0484
990.0313



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: CNhs12061


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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