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FF:11655-122E8: 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:Neurons, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC1525
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-Neural0.357
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-penis0.0445
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-lymphoma0.158
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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: CNhs13815

Jaspar motifP-value
MA0002.21.28472e-6
MA0003.10.103
MA0004.10.303
MA0006.10.389
MA0007.10.228
MA0009.10.4
MA0014.10.533
MA0017.10.00171
MA0018.20.00154
MA0019.10.321
MA0024.10.00216
MA0025.10.0235
MA0027.10.15
MA0028.10.538
MA0029.10.141
MA0030.10.0248
MA0031.10.00766
MA0035.20.0349
MA0038.10.0248
MA0039.20.0425
MA0040.10.0685
MA0041.10.345
MA0042.10.384
MA0043.10.173
MA0046.10.00614
MA0047.28.26015e-4
MA0048.10.724
MA0050.12.05324e-7
MA0051.19.49751e-4
MA0052.10.569
MA0055.10.485
MA0057.10.16
MA0058.10.192
MA0059.10.273
MA0060.15.03476e-4
MA0061.10.0158
MA0062.20.599
MA0065.23.55671e-4
MA0066.10.1
MA0067.10.471
MA0068.10.126
MA0069.10.56
MA0070.10.16
MA0071.10.117
MA0072.10.255
MA0073.10.209
MA0074.10.361
MA0076.10.257
MA0077.10.0475
MA0078.10.166
MA0079.20.431
MA0080.22.22698e-10
MA0081.10.0241
MA0083.10.78
MA0084.10.536
MA0087.10.195
MA0088.10.25
MA0090.10.0972
MA0091.10.707
MA0092.10.7
MA0093.10.323
MA0099.25.44825e-13
MA0100.10.659
MA0101.10.00724
MA0102.20.00304
MA0103.10.0941
MA0104.20.881
MA0105.10.0269
MA0106.10.0681
MA0107.10.00515
MA0108.20.103
MA0111.10.919
MA0112.21.07859e-4
MA0113.10.0698
MA0114.10.0122
MA0115.10.451
MA0116.10.0159
MA0117.10.665
MA0119.10.264
MA0122.10.32
MA0124.10.415
MA0125.10.147
MA0131.10.469
MA0135.10.135
MA0136.12.98405e-9
MA0137.20.322
MA0138.20.332
MA0139.10.399
MA0140.10.00106
MA0141.10.0208
MA0142.10.175
MA0143.10.171
MA0144.10.0482
MA0145.10.0701
MA0146.10.0155
MA0147.10.753
MA0148.10.0063
MA0149.10.0156
MA0150.18.14804e-5
MA0152.10.224
MA0153.10.13
MA0154.10.0239
MA0155.10.36
MA0156.11.24363e-7
MA0157.10.0224
MA0159.10.00269
MA0160.10.0109
MA0162.10.173
MA0163.10.00127
MA0164.10.754
MA0258.10.00542
MA0259.10.897



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: CNhs13815

Novel motifP-value
10.208
100.279
1000.938
1010.907
1020.861
1030.0549
1040.162
1050.0566
1060.0209
1070.158
1080.933
1090.00293
110.0812
1100.157
1110.913
1120.276
1130.79
1140.0625
1150.203
1160.944
1170.0655
1180.399
1190.326
120.505
1200.645
1210.203
1220.245
1230.201
1240.837
1250.22
1260.00842
1270.332
1280.114
1290.347
130.0193
1300.261
1310.466
1320.898
1330.532
1340.748
1350.537
1360.0364
1370.265
1380.48
1390.0537
140.77
1400.868
1410.467
1420.786
1430.103
1440.793
1450.482
1460.191
1470.959
1480.22
1490.198
150.0707
1500.5
1510.332
1520.082
1530.938
1540.61
1550.824
1560.636
1570.346
1580.943
1590.424
160.143
1600.172
1610.16
1620.745
1630.39
1640.0843
1650.393
1660.334
1670.358
1680.0989
1690.014
170.106
180.198
190.23
20.267
200.94
210.41
220.0757
230.0226
240.0586
250.55
260.153
270.33
280.783
290.169
30.114
300.402
310.916
320.0594
330.238
340.279
350.557
360.302
370.0783
380.165
390.305
40.869
400.0573
410.221
420.298
430.126
440.724
450.375
460.287
470.196
480.174
490.232
50.153
500.228
510.396
520.276
530.693
540.26
550.26
560.38
570.604
580.18
590.0217
60.97
600.0566
610.0554
620.158
630.106
640.507
650.155
660.632
670.641
680.284
690.555
70.161
700.0844
710.0398
720.279
730.0562
740.968
750.0834
760.727
770.0591
780.0345
790.741
80.412
800.0952
810.758
820.303
830.116
840.946
850.104
860.3
870.0561
880.686
890.253
90.21
900.904
910.732
920.128
930.59
940.45
950.0357
960.698
970.513
980.487
990.365



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: CNhs13815


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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