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FF:10181-103D1: 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 17:39, 29 March 2012


Name:spinal cord - adult, donor10196
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 stageNA
sexfemale
age60
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-Neural0.144
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-penis0.728
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-0.32
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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: CNhs13807

Jaspar motifP-value
MA0002.20.033
MA0003.10.219
MA0004.10.231
MA0006.10.512
MA0007.10.591
MA0009.10.134
MA0014.10.532
MA0017.10.0103
MA0018.20.151
MA0019.10.447
MA0024.10.667
MA0025.10.87
MA0027.10.841
MA0028.10.0113
MA0029.10.0415
MA0030.10.223
MA0031.10.502
MA0035.20.00418
MA0038.10.261
MA0039.20.154
MA0040.10.451
MA0041.10.54
MA0042.10.635
MA0043.10.749
MA0046.10.00244
MA0047.20.194
MA0048.10.0665
MA0050.10.0894
MA0051.10.223
MA0052.10.438
MA0055.18.02545e-5
MA0057.10.744
MA0058.10.294
MA0059.10.0808
MA0060.10.577
MA0061.10.00229
MA0062.26.97988e-5
MA0065.20.00243
MA0066.10.00863
MA0067.10.637
MA0068.10.802
MA0069.10.906
MA0070.10.179
MA0071.10.0217
MA0072.10.528
MA0073.10.497
MA0074.10.167
MA0076.10.0178
MA0077.10.0386
MA0078.10.739
MA0079.20.924
MA0080.23.84401e-7
MA0081.10.0264
MA0083.10.201
MA0084.10.217
MA0087.10.141
MA0088.10.124
MA0090.10.437
MA0091.10.675
MA0092.10.345
MA0093.10.281
MA0099.28.14996e-19
MA0100.10.381
MA0101.10.00144
MA0102.20.505
MA0103.10.0305
MA0104.20.302
MA0105.18.3745e-5
MA0106.10.0139
MA0107.10.00117
MA0108.20.466
MA0111.10.617
MA0112.20.00112
MA0113.10.711
MA0114.10.0124
MA0115.10.797
MA0116.10.00259
MA0117.10.926
MA0119.10.101
MA0122.10.612
MA0124.10.616
MA0125.10.15
MA0131.10.742
MA0135.10.0263
MA0136.11.35877e-11
MA0137.20.00942
MA0138.20.271
MA0139.10.482
MA0140.10.0062
MA0141.10.00737
MA0142.10.395
MA0143.10.0233
MA0144.10.725
MA0145.10.492
MA0146.10.018
MA0147.10.147
MA0148.10.19
MA0149.10.0125
MA0150.13.9474e-4
MA0152.10.671
MA0153.10.178
MA0154.10.0316
MA0155.10.777
MA0156.14.0817e-8
MA0157.10.958
MA0159.10.0196
MA0160.10.0235
MA0162.10.189
MA0163.18.63839e-8
MA0164.10.603
MA0258.10.00942
MA0259.10.563



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: CNhs13807

Novel motifP-value
10.0535
100.0743
1000.332
1010.641
1020.875
1030.0713
1040.0973
1050.114
1060.0945
1070.401
1080.795
1090.00103
110.0086
1100.042
1110.244
1120.553
1130.21
1140.137
1150.842
1160.179
1170.00621
1180.129
1190.286
120.287
1200.233
1210.577
1220.66
1230.818
1240.43
1250.458
1260.118
1270.579
1280.397
1290.67
130.00184
1300.221
1310.00858
1320.569
1330.015
1340.904
1350.104
1360.00237
1370.688
1380.889
1390.0549
140.772
1400.797
1410.637
1420.951
1430.0187
1440.737
1450.263
1460.389
1470.634
1480.805
1490.182
150.0387
1500.129
1510.769
1520.122
1530.98
1540.467
1550.542
1560.276
1570.38
1580.362
1590.023
160.0595
1600.277
1610.169
1620.715
1630.885
1640.00582
1650.183
1660.587
1670.964
1680.733
1690.025
170.0761
180.0912
190.409
20.954
200.155
210.0529
220.271
230.67
240.0409
250.647
260.00152
270.863
280.697
290.00612
30.0278
300.808
310.979
320.0386
330.0479
340.737
350.492
360.265
370.0339
380.341
390.498
40.947
400.077
410.248
420.178
430.143
440.189
450.725
460.0499
470.0568
480.0403
490.288
50.724
500.369
510.424
520.928
530.837
540.588
550.818
560.568
570.231
580.363
590.0851
60.952
600.209
610.0584
620.234
630.207
640.133
650.277
660.1
670.507
680.461
690.604
70.112
700.025
710.00843
720.322
730.0399
740.877
750.0132
760.171
770.179
780.00985
790.791
80.051
800.63
810.469
820.814
830.0609
840.338
850.611
860.134
872.66389e-4
880.677
890.256
90.557
900.141
910.666
920.703
930.508
940.134
950.0112
960.873
970.676
980.283
990.578



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: CNhs13807


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)
0007023 (adult organism)
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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