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FF:11250-116E8: 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 16:36, 29 March 2012


Name:Fibroblast - Pulmonary Artery, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepulmonary artery
dev stageNA
sexunknown
ageNA
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 numberlot:2546
catalog numberSC3125
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-0.129
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-lymphoma0.368
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: CNhs10878

Jaspar motifP-value
MA0002.20.144
MA0003.10.755
MA0004.10.256
MA0006.10.184
MA0007.10.0247
MA0009.10.605
MA0014.10.714
MA0017.10.78
MA0018.21.10077e-4
MA0019.10.374
MA0024.10.00503
MA0025.10.168
MA0027.10.999
MA0028.10.14
MA0029.10.652
MA0030.10.0308
MA0031.10.141
MA0035.20.464
MA0038.10.623
MA0039.20.773
MA0040.10.792
MA0041.10.563
MA0042.10.783
MA0043.14.16756e-4
MA0046.10.0797
MA0047.20.713
MA0048.10.0384
MA0050.13.93189e-5
MA0051.10.0437
MA0052.10.0455
MA0055.10.00178
MA0057.10.347
MA0058.10.077
MA0059.10.188
MA0060.10.223
MA0061.10.404
MA0062.20.146
MA0065.20.963
MA0066.10.39
MA0067.10.0095
MA0068.10.508
MA0069.10.706
MA0070.10.791
MA0071.10.907
MA0072.10.498
MA0073.10.718
MA0074.10.963
MA0076.10.86
MA0077.10.348
MA0078.10.478
MA0079.20.139
MA0080.25.63426e-6
MA0081.10.211
MA0083.10.00136
MA0084.10.0162
MA0087.10.449
MA0088.10.101
MA0090.19.00202e-4
MA0091.10.284
MA0092.10.0929
MA0093.10.223
MA0099.20.0734
MA0100.10.322
MA0101.10.179
MA0102.20.0183
MA0103.16.52831e-4
MA0104.20.618
MA0105.10.529
MA0106.10.189
MA0107.10.0942
MA0108.20.00179
MA0111.10.677
MA0112.20.0137
MA0113.10.0286
MA0114.10.374
MA0115.10.0983
MA0116.10.0509
MA0117.10.662
MA0119.10.0056
MA0122.10.924
MA0124.10.896
MA0125.10.81
MA0131.10.827
MA0135.10.027
MA0136.15.39846e-4
MA0137.20.837
MA0138.20.583
MA0139.10.771
MA0140.10.0464
MA0141.10.795
MA0142.10.868
MA0143.10.439
MA0144.10.418
MA0145.10.375
MA0146.10.755
MA0147.10.973
MA0148.10.608
MA0149.10.767
MA0150.10.707
MA0152.10.0141
MA0153.10.186
MA0154.10.462
MA0155.10.579
MA0156.10.105
MA0157.10.547
MA0159.10.39
MA0160.10.13
MA0162.10.0209
MA0163.10.0291
MA0164.10.559
MA0258.10.498
MA0259.10.36



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: CNhs10878

Novel motifP-value
10.234
100.521
1000.262
1010.499
1020.4
1030.113
1040.453
1050.494
1060.123
1070.0304
1080.819
1090.0541
110.299
1100.107
1110.147
1120.857
1130.124
1140.774
1150.446
1160.0902
1170.965
1180.774
1190.994
120.195
1200.178
1210.387
1220.558
1234.18901e-4
1240.412
1250.456
1260.749
1270.923
1280.78
1290.895
130.024
1300.048
1310.919
1320.619
1330.503
1340.305
1350.792
1360.199
1370.195
1380.246
1390.16
140.169
1400.983
1410.884
1420.421
1430.126
1440.516
1450.678
1460.347
1470.167
1480.181
1490.231
150.55
1500.0812
1510.952
1520.0702
1530.477
1540.435
1550.0543
1560.717
1570.0909
1580.00656
1590.154
160.0764
1600.0273
1610.922
1620.77
1630.596
1640.533
1650.825
1660.449
1670.728
1680.482
1690.098
170.476
180.502
190.0513
20.699
200.898
210.269
220.75
230.736
240.0738
250.705
260.207
270.931
280.122
290.263
30.306
300.836
310.864
321.52994e-5
330.0579
340.866
350.291
360.552
370.0762
380.9
390.0716
40.822
400.47
410.67
420.378
430.886
440.165
450.683
460.185
470.432
480.214
490.749
50.472
500.656
510.926
520.77
530.135
540.654
550.684
560.825
570.535
580.22
590.378
60.6
600.668
610.9
620.63
630.222
640.593
650.954
660.182
670.504
680.675
690.35
70.697
700.596
710.137
720.5
730.00837
740.486
750.486
760.413
770.154
780.629
790.0878
80.0158
800.68
810.986
820.661
830.247
840.495
850.963
860.754
870.0122
880.62
890.24
90.855
900.808
910.716
920.991
930.777
940.715
950.0193
960.718
970.544
980.0929
990.00161



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: CNhs10878


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)
0002557 (fibroblast of pulmonary artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
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)
0001637 (artery)
0001981 (blood vessel)
0002012 (pulmonary artery)
0002049 (vasculature)
0002050 (embryonic structure)
0002061 (truncus arteriosus)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004145 (outflow tract)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004572 (arterial system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0006965 (vascular cord)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008886 (pulmonary vascular system)

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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