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FF:10153-102I9: 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 17:14, 29 March 2012


Name:hippocampus, adult, donor10252
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
age76
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-Neural0.373
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-penis1.032
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-0.323
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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: CNhs12312

Jaspar motifP-value
MA0002.20.0184
MA0003.10.219
MA0004.10.336
MA0006.10.323
MA0007.10.416
MA0009.10.0887
MA0014.10.64
MA0017.10.00129
MA0018.20.732
MA0019.10.639
MA0024.10.998
MA0025.10.774
MA0027.10.384
MA0028.10.0529
MA0029.10.0143
MA0030.10.494
MA0031.10.937
MA0035.20.00379
MA0038.10.384
MA0039.20.178
MA0040.10.677
MA0041.10.44
MA0042.10.972
MA0043.10.602
MA0046.10.0055
MA0047.20.0581
MA0048.10.184
MA0050.10.0543
MA0051.10.152
MA0052.10.455
MA0055.10.00329
MA0057.10.808
MA0058.10.29
MA0059.10.0704
MA0060.10.775
MA0061.10.00757
MA0062.20.00153
MA0065.22.75607e-4
MA0066.10.0093
MA0067.10.949
MA0068.10.779
MA0069.10.433
MA0070.10.619
MA0071.10.0208
MA0072.10.299
MA0073.10.383
MA0074.10.261
MA0076.10.089
MA0077.10.0915
MA0078.10.737
MA0079.20.615
MA0080.26.11493e-8
MA0081.10.0328
MA0083.10.0147
MA0084.10.556
MA0087.10.597
MA0088.10.159
MA0090.10.455
MA0091.10.481
MA0092.10.271
MA0093.10.356
MA0099.25.76308e-21
MA0100.10.511
MA0101.10.0036
MA0102.20.157
MA0103.10.127
MA0104.20.371
MA0105.17.83264e-4
MA0106.10.0229
MA0107.10.00398
MA0108.20.228
MA0111.10.52
MA0112.26.34971e-4
MA0113.10.53
MA0114.10.00221
MA0115.10.559
MA0116.10.00676
MA0117.10.796
MA0119.10.133
MA0122.10.839
MA0124.10.579
MA0125.10.208
MA0131.10.963
MA0135.10.0198
MA0136.14.02178e-12
MA0137.20.911
MA0138.20.494
MA0139.10.372
MA0140.13.55621e-4
MA0141.10.00328
MA0142.10.82
MA0143.10.459
MA0144.10.349
MA0145.10.191
MA0146.10.0178
MA0147.10.243
MA0148.10.0599
MA0149.10.017
MA0150.13.94687e-5
MA0152.10.525
MA0153.10.221
MA0154.10.0454
MA0155.10.639
MA0156.14.45064e-8
MA0157.10.551
MA0159.10.00501
MA0160.10.00702
MA0162.10.113
MA0163.13.66737e-6
MA0164.10.735
MA0258.10.0093
MA0259.10.669



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: CNhs12312

Novel motifP-value
10.0445
100.05
1000.369
1010.503
1020.983
1030.116
1040.107
1050.16
1060.0475
1070.141
1080.881
1090.00128
110.01
1100.0501
1110.0881
1120.281
1130.656
1140.104
1150.974
1160.182
1170.0123
1180.139
1190.215
120.587
1200.208
1210.335
1220.737
1230.977
1240.39
1250.318
1260.0413
1270.405
1280.244
1290.546
130.00261
1300.304
1310.0603
1320.491
1330.113
1340.577
1350.481
1360.00235
1370.724
1380.807
1390.168
140.819
1400.744
1410.385
1420.601
1430.0334
1440.992
1450.185
1460.543
1470.899
1480.212
1490.275
150.0736
1500.164
1510.565
1520.0954
1530.996
1540.54
1550.583
1560.339
1570.44
1580.405
1590.0271
160.0432
1600.218
1610.198
1620.745
1630.896
1640.0354
1650.0959
1660.713
1670.734
1680.459
1690.00981
170.107
180.0817
190.197
20.847
200.204
210.0456
220.224
230.412
240.0517
250.42
269.72582e-4
270.702
280.674
290.00663
30.0464
300.849
310.858
320.0256
330.0466
340.684
350.582
360.136
370.0353
380.353
390.33
40.635
400.0278
410.272
420.199
430.126
440.151
450.696
460.0729
470.058
480.0518
490.214
50.62
500.384
510.373
520.546
530.874
540.369
550.725
560.503
570.348
580.292
590.0644
60.909
600.0682
610.0988
620.185
630.196
640.154
650.248
660.117
670.257
680.173
690.342
70.0554
700.0497
710.0109
720.39
730.0295
740.97
750.0259
760.352
770.171
780.00124
790.271
80.0782
800.439
810.606
820.608
830.017
840.556
850.242
860.209
871.81986e-4
880.807
890.279
90.413
900.105
910.875
920.486
930.977
940.184
950.00919
960.909
970.796
980.252
990.567



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: CNhs12312


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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