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FF:10033-101E6: 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 16:28, 29 March 2012


Name:pons, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepons
dev stage18-54 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101345A
catalog numberCat:636572
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Neural0.189
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-penis0.0854
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-0.296
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0806
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10640

Jaspar motifP-value
MA0002.20.0159
MA0003.10.337
MA0004.10.337
MA0006.10.441
MA0007.10.255
MA0009.10.201
MA0014.10.831
MA0017.10.00819
MA0018.20.0493
MA0019.10.464
MA0024.10.854
MA0025.10.247
MA0027.10.506
MA0028.10.192
MA0029.10.161
MA0030.10.0388
MA0031.10.4
MA0035.20.081
MA0038.10.0287
MA0039.20.516
MA0040.10.246
MA0041.10.157
MA0042.10.507
MA0043.10.327
MA0046.10.0848
MA0047.20.32
MA0048.10.0621
MA0050.10.0335
MA0051.10.192
MA0052.10.29
MA0055.10.00194
MA0057.10.874
MA0058.10.421
MA0059.10.0824
MA0060.10.053
MA0061.10.00552
MA0062.20.0655
MA0065.27.32435e-4
MA0066.10.0191
MA0067.10.482
MA0068.10.733
MA0069.10.556
MA0070.10.18
MA0071.10.0361
MA0072.10.679
MA0073.10.513
MA0074.10.168
MA0076.10.474
MA0077.10.0888
MA0078.10.918
MA0079.20.342
MA0080.28.30565e-7
MA0081.10.117
MA0083.10.0915
MA0084.10.337
MA0087.10.253
MA0088.10.188
MA0090.10.231
MA0091.10.405
MA0092.10.33
MA0093.10.406
MA0099.22.86734e-11
MA0100.10.741
MA0101.10.00533
MA0102.20.357
MA0103.10.159
MA0104.20.412
MA0105.11.1716e-4
MA0106.10.0208
MA0107.10.00629
MA0108.20.494
MA0111.10.493
MA0112.20.00128
MA0113.10.353
MA0114.10.00835
MA0115.10.714
MA0116.10.00207
MA0117.10.886
MA0119.10.0509
MA0122.10.957
MA0124.10.629
MA0125.10.218
MA0131.10.954
MA0135.10.0263
MA0136.14.06234e-8
MA0137.20.708
MA0138.20.126
MA0139.10.427
MA0140.10.0714
MA0141.10.0197
MA0142.10.806
MA0143.10.318
MA0144.10.497
MA0145.10.381
MA0146.10.0215
MA0147.10.258
MA0148.10.3
MA0149.10.0162
MA0150.10.00536
MA0152.10.967
MA0153.10.483
MA0154.10.028
MA0155.10.603
MA0156.12.64796e-4
MA0157.10.818
MA0159.10.00844
MA0160.10.0829
MA0162.10.141
MA0163.12.39488e-7
MA0164.10.617
MA0258.10.0156
MA0259.10.745



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: CNhs10640

Novel motifP-value
10.0385
100.0261
1000.235
1010.876
1020.805
1030.262
1040.126
1050.246
1060.0292
1070.0964
1080.857
1090.0152
110.0158
1100.028
1110.143
1120.368
1130.697
1140.111
1150.92
1160.174
1170.00803
1180.12
1190.156
120.745
1200.12
1210.986
1220.579
1230.627
1240.022
1250.237
1260.0652
1270.577
1280.187
1290.522
130.00134
1300.624
1310.0547
1320.795
1330.00546
1340.261
1350.0908
1360.025
1370.75
1380.807
1390.0669
140.973
1400.181
1410.316
1420.877
1430.0303
1440.928
1450.0595
1460.663
1470.783
1480.155
1490.253
150.0618
1500.142
1510.761
1520.191
1530.804
1540.647
1550.401
1560.439
1570.393
1580.358
1590.00743
160.0662
1600.162
1610.283
1620.84
1630.973
1640.0083
1650.221
1660.853
1670.357
1680.667
1690.0129
170.101
180.153
190.27
20.966
200.0722
210.0636
220.326
230.43
240.107
250.561
266.66356e-6
270.935
280.831
290.0122
30.045
300.63
310.909
320.0168
330.0822
340.761
350.425
360.0996
370.0583
380.379
390.222
40.96
400.0581
410.323
420.245
430.102
440.087
450.798
460.0303
470.0767
480.0605
490.156
50.645
500.353
510.464
520.667
530.963
540.503
550.344
560.541
570.233
580.361
590.102
60.798
600.0763
610.08
620.18
630.153
640.185
650.306
660.326
670.505
680.333
690.461
70.0648
700.012
710.00547
720.467
730.0775
740.734
750.0265
760.271
770.218
780.00303
790.192
80.0383
800.79
810.485
820.428
830.254
840.46
850.3
860.182
870.0128
880.831
890.388
90.494
900.0388
910.473
920.395
930.811
940.0426
950.0634
960.868
970.69
980.172
990.575



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: CNhs10640


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)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000988 (pons)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001895 (metencephalon)
0002028 (hindbrain)
0002050 (embryonic structure)
0002298 (brainstem)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002680 (regional part of metencephalon)
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)
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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