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FF:11417-118F4: Difference between revisions

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|creation_date=
|creation_date=
|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 17:07, 29 March 2012


Name:Fibroblast - Cardiac, donor3
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 stage20 weeks old fetus
sexfemale
ageembryo 20week
cell typefibroblast
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1994
catalog numberCA306-R10f
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-penis0.0863
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-lymphoma-0.234
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12027

Jaspar motifP-value
MA0002.20.741
MA0003.10.234
MA0004.10.845
MA0006.10.0427
MA0007.10.408
MA0009.10.159
MA0014.10.662
MA0017.10.876
MA0018.20.00115
MA0019.10.126
MA0024.11.28465e-4
MA0025.10.324
MA0027.10.24
MA0028.10.533
MA0029.10.0903
MA0030.10.139
MA0031.10.0223
MA0035.20.977
MA0038.10.155
MA0039.20.863
MA0040.10.609
MA0041.10.397
MA0042.10.817
MA0043.19.47502e-4
MA0046.10.463
MA0047.20.883
MA0048.10.209
MA0050.10.00986
MA0051.10.265
MA0052.10.712
MA0055.10.318
MA0057.10.198
MA0058.10.593
MA0059.10.612
MA0060.10.0154
MA0061.10.562
MA0062.20.0294
MA0065.20.477
MA0066.10.261
MA0067.10.017
MA0068.10.203
MA0069.10.438
MA0070.10.273
MA0071.10.801
MA0072.10.861
MA0073.10.758
MA0074.10.133
MA0076.10.188
MA0077.10.121
MA0078.10.373
MA0079.20.191
MA0080.25.70045e-7
MA0081.10.023
MA0083.10.0174
MA0084.10.43
MA0087.10.769
MA0088.10.845
MA0090.10.00681
MA0091.10.253
MA0092.10.499
MA0093.10.841
MA0099.20.379
MA0100.10.106
MA0101.10.351
MA0102.23.85922e-4
MA0103.10.842
MA0104.20.109
MA0105.10.475
MA0106.10.361
MA0107.10.405
MA0108.20.00252
MA0111.10.0912
MA0112.20.0225
MA0113.10.365
MA0114.10.269
MA0115.10.165
MA0116.10.792
MA0117.10.237
MA0119.10.642
MA0122.10.638
MA0124.10.112
MA0125.10.255
MA0131.10.0982
MA0135.10.405
MA0136.11.4726e-7
MA0137.20.0749
MA0138.20.315
MA0139.10.48
MA0140.10.638
MA0141.10.202
MA0142.10.124
MA0143.10.371
MA0144.10.656
MA0145.10.36
MA0146.10.192
MA0147.10.207
MA0148.10.578
MA0149.10.763
MA0150.10.14
MA0152.10.417
MA0153.10.549
MA0154.10.415
MA0155.10.034
MA0156.10.00129
MA0157.10.0289
MA0159.10.271
MA0160.10.503
MA0162.10.0654
MA0163.10.178
MA0164.10.576
MA0258.10.0465
MA0259.10.276



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: CNhs12027

Novel motifP-value
10.989
100.26
1000.57
1010.297
1020.5
1030.674
1040.43
1050.549
1060.108
1070.0659
1080.148
1090.0586
110.34
1100.672
1110.743
1120.597
1130.0425
1140.682
1150.00411
1160.106
1170.848
1180.68
1190.643
120.741
1200.0615
1210.893
1220.333
1238.62972e-4
1240.166
1250.931
1260.925
1270.633
1280.616
1290.748
130.961
1300.755
1310.455
1320.523
1330.558
1340.567
1350.856
1360.182
1370.0904
1380.445
1390.999
140.568
1400.497
1410.342
1420.418
1430.0576
1440.745
1450.709
1460.834
1470.143
1480.292
1490.0125
150.738
1500.0393
1510.955
1520.00532
1530.335
1540.586
1550.31
1560.696
1570.376
1580.038
1590.875
160.084
1600.334
1610.406
1620.485
1630.812
1640.238
1650.208
1660.717
1670.668
1680.528
1690.0725
170.35
180.255
190.0781
20.407
200.592
210.41
220.262
230.787
240.928
250.159
260.556
270.369
280.154
290.465
30.835
300.441
310.283
326.62059e-15
330.822
340.558
350.529
360.337
370.0956
380.651
390.563
40.641
400.534
410.766
420.335
430.933
440.134
450.455
460.501
470.857
480.377
490.425
50.773
500.935
510.718
520.911
530.12
540.553
550.417
560.992
570.831
580.105
590.0421
60.912
600.898
610.778
620.279
630.768
640.766
650.372
660.623
670.839
680.481
690.196
70.326
700.639
710.79
720.357
730.00116
740.897
750.945
760.357
770.0155
780.942
791.65658e-4
80.17
800.631
810.71
820.566
830.128
840.304
850.22
860.858
870.00583
880.601
890.0169
90.913
900.0354
910.704
920.906
930.929
940.715
950.0914
960.209
970.627
980.335
990.0201



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: CNhs12027


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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