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FF:10046-101G1: 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 16:30, 29 March 2012


Name:heart, fetal, pool1
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 stage12-31 weeks fetus
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number9041413A
catalog numberCat:636583
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-penis0.0282
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-0.0557
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.126
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs10653

Jaspar motifP-value
MA0002.24.14702e-4
MA0003.10.956
MA0004.10.0632
MA0006.10.861
MA0007.10.57
MA0009.10.373
MA0014.10.678
MA0017.10.211
MA0018.20.233
MA0019.10.262
MA0024.10.758
MA0025.10.882
MA0027.10.848
MA0028.14.96826e-4
MA0029.10.05
MA0030.10.433
MA0031.10.47
MA0035.22.08313e-5
MA0038.10.344
MA0039.20.619
MA0040.10.773
MA0041.10.139
MA0042.10.3
MA0043.10.669
MA0046.10.346
MA0047.20.42
MA0048.10.201
MA0050.10.00169
MA0051.10.0132
MA0052.16.354e-50
MA0055.10.038
MA0057.10.768
MA0058.10.0383
MA0059.10.00119
MA0060.10.219
MA0061.19.09014e-4
MA0062.26.21372e-7
MA0065.20.0144
MA0066.10.336
MA0067.10.836
MA0068.10.00351
MA0069.10.741
MA0070.10.156
MA0071.10.755
MA0072.10.702
MA0073.10.598
MA0074.10.662
MA0076.12.64449e-4
MA0077.10.432
MA0078.10.387
MA0079.20.26
MA0080.28.59382e-5
MA0081.10.103
MA0083.11.03937e-6
MA0084.10.614
MA0087.10.338
MA0088.10.0416
MA0090.10.00421
MA0091.10.851
MA0092.10.979
MA0093.10.0651
MA0099.25.30907e-16
MA0100.10.861
MA0101.10.0283
MA0102.20.137
MA0103.10.00727
MA0104.20.00669
MA0105.13.85394e-7
MA0106.10.0333
MA0107.10.0205
MA0108.22.3507e-21
MA0111.10.897
MA0112.20.0261
MA0113.10.248
MA0114.10.0653
MA0115.10.659
MA0116.13.43892e-4
MA0117.10.815
MA0119.10.791
MA0122.10.0599
MA0124.10.339
MA0125.10.609
MA0131.10.801
MA0135.10.439
MA0136.11.4859e-7
MA0137.20.616
MA0138.20.381
MA0139.10.0476
MA0140.10.00106
MA0141.10.321
MA0142.10.0112
MA0143.10.0799
MA0144.10.514
MA0145.10.808
MA0146.10.0497
MA0147.10.00211
MA0148.10.928
MA0149.10.0378
MA0150.12.31484e-5
MA0152.10.417
MA0153.10.503
MA0154.10.0748
MA0155.10.791
MA0156.11.67061e-5
MA0157.10.645
MA0159.10.36
MA0160.10.445
MA0162.10.268
MA0163.11.00365e-9
MA0164.10.421
MA0258.10.347
MA0259.10.177



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: CNhs10653

Novel motifP-value
10.0246
100.0201
1000.407
1010.573
1020.695
1030.0877
1040.319
1050.323
1060.18
1070.669
1080.858
1090.0074
110.0376
1100.0769
1110.0012
1120.422
1130.171
1140.0603
1150.97
1160.306
1170.00522
1180.0222
1190.158
120.966
1200.0633
1210.509
1220.487
1230.0377
1240.96
1250.22
1260.281
1270.308
1280.445
1290.167
130.123
1300.206
1310.00538
1320.406
1330.11
1340.0589
1350.193
1360.0344
1370.277
1380.57
1390.176
140.81
1400.9
1410.248
1420.996
1430.00203
1440.851
1450.402
1460.76
1470.272
1480.0564
1490.887
150.0781
1500.361
1510.725
1520.282
1530.38
1540.901
1550.192
1560.931
1570.659
1580.972
1590.839
160.0409
1600.523
1610.391
1620.768
1630.426
1640.00743
1650.437
1660.0569
1670.0214
1680.307
1690.00404
170.212
180.0434
190.866
20.636
200.118
210.322
220.791
230.766
240.268
250.38
260.00172
270.42
280.671
290.00379
30.0497
300.292
310.467
320.472
330.22
340.289
350.476
360.0833
370.0805
380.435
390.489
40.737
400.115
410.529
420.185
430.0751
440.364
450.569
460.0703
470.0301
480.0529
490.12
50.577
500.964
510.652
520.54
530.844
540.979
550.153
560.34
570.11
580.326
590.404
60.742
600.59
610.0545
620.325
630.254
640.156
650.668
660.148
670.461
680.861
690.621
70.494
700.00192
710.0107
720.39
730.044
740.129
750.0146
760.0875
770.55
780.698
790.703
80.0461
800.17
810.105
820.26
830.546
840.634
850.638
860.503
870.00295
880.978
890.469
90.972
900.00408
910.492
920.394
930.446
940.0152
950.0115
960.464
970.795
980.311
990.602



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: CNhs10653


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

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)
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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