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FF:10169-103B7: 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 17:38, 29 March 2012


Name:hippocampus - 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
tissuehippocampus
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-Neural0.413
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-penis0.782
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-0.382
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs13795

Jaspar motifP-value
MA0002.20.0624
MA0003.10.285
MA0004.10.323
MA0006.10.215
MA0007.10.313
MA0009.10.268
MA0014.10.616
MA0017.10.00671
MA0018.20.278
MA0019.10.497
MA0024.10.684
MA0025.10.781
MA0027.10.568
MA0028.10.0202
MA0029.10.0546
MA0030.10.714
MA0031.10.285
MA0035.20.0097
MA0038.10.474
MA0039.20.0767
MA0040.10.611
MA0041.10.475
MA0042.10.924
MA0043.10.714
MA0046.10.00235
MA0047.20.0195
MA0048.10.0986
MA0050.10.0199
MA0051.10.0847
MA0052.10.916
MA0055.10.00112
MA0057.10.81
MA0058.10.23
MA0059.10.097
MA0060.10.689
MA0061.10.00783
MA0062.22.24028e-4
MA0065.27.47772e-4
MA0066.10.0278
MA0067.10.98
MA0068.10.853
MA0069.10.44
MA0070.10.73
MA0071.10.00661
MA0072.10.146
MA0073.10.443
MA0074.10.18
MA0076.10.0445
MA0077.10.194
MA0078.10.862
MA0079.20.997
MA0080.27.9548e-9
MA0081.10.0336
MA0083.10.0361
MA0084.10.895
MA0087.10.722
MA0088.10.208
MA0090.10.211
MA0091.10.637
MA0092.10.426
MA0093.10.311
MA0099.28.78978e-19
MA0100.10.63
MA0101.10.00101
MA0102.20.188
MA0103.10.173
MA0104.20.541
MA0105.10.00812
MA0106.10.0267
MA0107.10.00243
MA0108.20.404
MA0111.10.58
MA0112.20.0026
MA0113.10.604
MA0114.10.00301
MA0115.10.514
MA0116.10.0145
MA0117.10.949
MA0119.10.137
MA0122.10.426
MA0124.10.605
MA0125.10.123
MA0131.10.662
MA0135.10.0292
MA0136.12.66059e-13
MA0137.20.793
MA0138.20.225
MA0139.10.338
MA0140.16.78724e-4
MA0141.10.0102
MA0142.10.473
MA0143.10.31
MA0144.10.331
MA0145.10.187
MA0146.10.00527
MA0147.10.372
MA0148.10.0238
MA0149.10.0579
MA0150.18.68483e-5
MA0152.10.393
MA0153.10.145
MA0154.10.0578
MA0155.10.582
MA0156.12.83896e-10
MA0157.10.178
MA0159.10.00757
MA0160.10.0129
MA0162.10.131
MA0163.11.21673e-4
MA0164.10.583
MA0258.10.0188
MA0259.10.869



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: CNhs13795

Novel motifP-value
10.0771
100.0521
1000.368
1010.241
1020.897
1030.221
1040.168
1050.136
1060.0302
1070.105
1080.981
1090.00146
110.0124
1100.0493
1110.281
1120.594
1130.378
1140.325
1150.854
1160.063
1170.00618
1180.123
1190.223
120.505
1200.23
1210.0772
1220.725
1230.897
1240.0282
1250.348
1260.0223
1270.425
1280.206
1290.485
136.77604e-4
1300.135
1310.0836
1320.677
1330.0012
1340.366
1350.0659
1365.85162e-4
1370.868
1380.892
1390.15
140.808
1400.503
1410.514
1420.666
1430.0926
1440.79
1450.0913
1460.331
1470.795
1480.265
1490.205
150.111
1500.134
1510.568
1520.0561
1530.609
1540.313
1550.727
1560.339
1570.406
1580.233
1590.0274
160.0494
1600.275
1610.251
1620.707
1630.918
1640.0132
1650.0484
1660.696
1670.685
1680.295
1690.0132
170.113
180.159
190.187
20.73
200.133
210.0773
220.152
230.401
240.0152
250.605
263.36067e-5
270.989
280.744
290.0091
30.0544
300.922
310.957
320.0416
330.0423
340.7
350.733
360.289
370.0305
380.261
390.249
40.895
400.0364
410.441
420.277
430.121
440.154
450.591
460.0738
470.0541
480.0377
490.21
50.78
500.173
510.523
520.536
530.836
540.348
550.771
560.53
570.41
580.406
590.0394
60.917
600.0755
610.049
620.268
630.163
640.191
650.224
660.121
670.224
680.149
690.559
70.0565
700.037
710.0127
720.311
730.0203
740.917
750.0191
760.42
770.125
784.49413e-4
790.338
80.108
800.436
810.825
820.682
830.012
840.535
850.272
860.154
878.1062e-5
880.766
890.5
90.363
900.265
910.843
920.841
930.497
940.426
950.00833
960.775
970.599
980.351
990.43



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: CNhs13795


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)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000349 (limbic system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0001954 (Ammon's horn)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002421 (hippocampal formation)
0002532 (epiblast (generic))
0002600 (limbic lobe)
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003022 (lobe parts of cerebral cortex)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
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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