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FF:10174-103C3: 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:medulla oblongata - 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
tissuemedulla oblongata
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-Neural9.491671e-4
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-penis0.883
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs13800

Jaspar motifP-value
MA0002.20.0156
MA0003.10.229
MA0004.10.159
MA0006.10.623
MA0007.10.681
MA0009.10.203
MA0014.10.787
MA0017.10.0437
MA0018.20.0509
MA0019.10.649
MA0024.10.981
MA0025.10.894
MA0027.10.149
MA0028.10.0301
MA0029.10.0975
MA0030.10.177
MA0031.10.568
MA0035.20.0164
MA0038.10.191
MA0039.20.419
MA0040.10.71
MA0041.10.723
MA0042.10.706
MA0043.10.999
MA0046.10.0928
MA0047.20.202
MA0048.10.0991
MA0050.10.0284
MA0051.10.141
MA0052.10.643
MA0055.10.00246
MA0057.10.992
MA0058.10.165
MA0059.10.0462
MA0060.10.613
MA0061.10.00221
MA0062.28.31146e-5
MA0065.20.00322
MA0066.10.0402
MA0067.10.623
MA0068.10.928
MA0069.10.666
MA0070.10.798
MA0071.10.0864
MA0072.10.849
MA0073.10.507
MA0074.10.218
MA0076.10.0561
MA0077.10.0341
MA0078.10.955
MA0079.20.998
MA0080.21.92145e-8
MA0081.10.0147
MA0083.10.079
MA0084.10.192
MA0087.10.0682
MA0088.10.145
MA0090.10.886
MA0091.10.221
MA0092.10.26
MA0093.10.212
MA0099.23.08268e-18
MA0100.10.551
MA0101.10.00107
MA0102.20.411
MA0103.10.0905
MA0104.20.228
MA0105.14.24989e-5
MA0106.10.0127
MA0107.19.84754e-4
MA0108.20.0864
MA0111.10.785
MA0112.20.00158
MA0113.10.835
MA0114.10.0314
MA0115.10.973
MA0116.10.00296
MA0117.10.714
MA0119.10.221
MA0122.10.232
MA0124.10.766
MA0125.10.0565
MA0131.10.886
MA0135.10.00252
MA0136.11.31597e-11
MA0137.20.00262
MA0138.20.272
MA0139.10.592
MA0140.10.0208
MA0141.10.0496
MA0142.10.221
MA0143.10.0165
MA0144.10.643
MA0145.10.369
MA0146.10.0144
MA0147.10.108
MA0148.10.233
MA0149.10.0267
MA0150.11.18537e-4
MA0152.10.215
MA0153.10.728
MA0154.10.0264
MA0155.10.624
MA0156.11.2805e-8
MA0157.10.943
MA0159.10.036
MA0160.10.166
MA0162.10.184
MA0163.11.14012e-8
MA0164.10.412
MA0258.10.0258
MA0259.10.486



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: CNhs13800

Novel motifP-value
10.0542
100.0408
1000.485
1010.358
1020.904
1030.0156
1040.0426
1050.422
1060.0441
1070.256
1080.853
1090.00528
110.00917
1100.0507
1110.106
1120.703
1130.123
1140.0927
1150.709
1160.114
1170.00614
1180.143
1190.209
120.555
1200.118
1210.728
1220.776
1230.706
1240.215
1250.602
1260.262
1270.418
1280.45
1290.784
130.00769
1300.143
1310.0977
1320.319
1330.0572
1340.742
1350.0913
1360.0137
1370.72
1380.457
1390.0967
140.96
1400.981
1410.67
1420.801
1430.00973
1440.666
1450.369
1460.464
1470.805
1480.719
1490.106
150.065
1500.126
1510.647
1520.127
1530.723
1540.5
1550.383
1560.281
1570.352
1580.297
1590.0189
160.0581
1600.126
1610.125
1620.781
1630.721
1640.00633
1650.205
1660.385
1670.902
1680.467
1690.0169
170.0562
180.0211
190.416
20.877
200.23
210.0274
220.276
230.676
240.0837
250.593
269.29189e-4
270.663
280.954
290.00596
30.0294
300.604
310.647
320.00942
330.114
340.653
350.323
360.248
370.0351
380.412
390.615
40.673
400.11
410.272
420.208
430.0961
440.183
450.768
460.0218
470.0408
480.0266
490.208
50.866
500.4
510.197
520.917
530.644
540.377
550.985
560.629
570.322
580.487
590.0515
60.987
600.206
610.0697
620.209
630.226
640.142
650.232
660.0774
670.29
680.515
690.398
70.179
700.0261
710.00739
720.391
730.0491
740.803
750.00763
760.171
770.276
783.52932e-4
790.44
80.0804
800.573
810.435
820.882
830.0267
840.391
850.615
860.108
874.00928e-4
880.56
890.097
90.661
900.146
910.551
920.814
930.683
940.0874
950.0257
960.993
970.851
980.196
990.659



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: CNhs13800


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)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001896 (medulla oblongata)
0002028 (hindbrain)
0002050 (embryonic structure)
0002298 (brainstem)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
0005290 (myelencephalon)
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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