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FF:10056-101H2: 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 16:52, 29 March 2012


Name:spinal cord, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
dev stage29 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA703261
catalog numberCat:RtHFN: Spinal cord
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-Neural0.266
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-penis0.088
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-0.127
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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: CNhs11764

Jaspar motifP-value
MA0002.26.14425e-4
MA0003.10.297
MA0004.10.196
MA0006.10.738
MA0007.10.445
MA0009.10.0877
MA0014.10.306
MA0017.10.0118
MA0018.20.259
MA0019.10.762
MA0024.10.421
MA0025.10.481
MA0027.10.569
MA0028.10.0149
MA0029.10.248
MA0030.10.853
MA0031.10.182
MA0035.20.0654
MA0038.10.144
MA0039.20.148
MA0040.10.647
MA0041.10.611
MA0042.10.993
MA0043.10.438
MA0046.10.0366
MA0047.20.00799
MA0048.10.205
MA0050.10.00216
MA0051.10.0497
MA0052.10.374
MA0055.10.00322
MA0057.10.693
MA0058.10.187
MA0059.10.0462
MA0060.10.15
MA0061.10.00513
MA0062.26.7581e-5
MA0065.20.00146
MA0066.10.0271
MA0067.10.652
MA0068.10.0219
MA0069.10.741
MA0070.10.404
MA0071.10.122
MA0072.10.277
MA0073.10.51
MA0074.10.278
MA0076.10.0146
MA0077.10.0613
MA0078.10.838
MA0079.20.671
MA0080.22.23987e-9
MA0081.10.0251
MA0083.10.778
MA0084.10.171
MA0087.10.187
MA0088.10.0601
MA0090.10.782
MA0091.10.645
MA0092.10.392
MA0093.10.226
MA0099.24.70196e-20
MA0100.10.423
MA0101.10.00115
MA0102.20.0382
MA0103.10.0823
MA0104.20.166
MA0105.16.03532e-5
MA0106.10.026
MA0107.10.00295
MA0108.23.55082e-5
MA0111.10.666
MA0112.29.35709e-4
MA0113.10.462
MA0114.10.0103
MA0115.10.215
MA0116.10.00168
MA0117.10.655
MA0119.10.0557
MA0122.10.718
MA0124.10.46
MA0125.10.197
MA0131.10.856
MA0135.10.164
MA0136.15.01209e-16
MA0137.20.581
MA0138.20.182
MA0139.10.209
MA0140.10.0252
MA0141.10.0112
MA0142.10.619
MA0143.10.247
MA0144.10.302
MA0145.10.353
MA0146.10.0132
MA0147.10.0882
MA0148.10.0394
MA0149.10.00609
MA0150.15.11222e-7
MA0152.10.234
MA0153.10.915
MA0154.10.0139
MA0155.10.823
MA0156.16.88429e-10
MA0157.10.118
MA0159.10.00749
MA0160.10.0177
MA0162.10.226
MA0163.11.39833e-7
MA0164.10.573
MA0258.10.0203
MA0259.10.446



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: CNhs11764

Novel motifP-value
10.0296
100.0353
1000.375
1010.903
1020.899
1030.0636
1040.239
1050.162
1060.157
1070.541
1080.765
1090.00259
110.0154
1100.0434
1110.131
1120.394
1130.266
1140.0313
1150.331
1160.47
1170.00393
1180.0897
1190.149
120.539
1200.161
1210.735
1220.736
1230.56
1240.393
1250.462
1260.106
1270.176
1280.45
1290.467
130.00685
1300.418
1310.24
1320.349
1330.0817
1340.645
1350.263
1360.0402
1370.316
1380.567
1390.0812
140.668
1400.186
1410.218
1420.784
1430.00108
1440.947
1450.396
1460.585
1470.767
1480.193
1490.163
150.0341
1500.239
1510.662
1520.174
1530.451
1540.664
1550.216
1560.427
1570.479
1580.752
1590.155
160.134
1600.257
1610.149
1620.551
1630.524
1640.0359
1650.352
1660.255
1670.239
1680.625
1690.0109
170.128
180.0657
190.415
20.932
200.15
210.16
220.283
230.484
240.0494
250.47
265.32485e-4
270.664
280.507
290.00809
30.031
300.437
310.917
320.801
330.0939
340.997
350.391
360.103
370.0292
380.254
390.805
40.936
400.0557
410.155
420.123
430.131
440.252
450.852
460.0516
470.0426
480.0697
490.13
50.319
500.576
510.39
520.931
530.899
540.466
550.242
560.52
570.313
580.22
590.207
60.977
600.195
610.0828
620.13
630.194
640.202
650.302
660.11
670.302
680.348
690.763
70.105
700.0109
710.00779
720.222
730.0394
740.793
750.0133
760.149
770.239
780.00829
790.998
80.103
800.686
810.583
820.545
830.358
840.677
850.391
860.136
870.00488
880.731
890.427
90.649
900.0698
910.794
920.398
930.297
940.058
950.0114
960.318
970.891
980.11
990.787



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: CNhs11764


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)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001137 (dorsum)
0002050 (embryonic structure)
0002100 (trunk)
0002240 (spinal cord)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0003103 (compound organ)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005174 (dorsal region element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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