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FF:13323-143B2: 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:Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor3 (536_119:Ud_0h)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexn/a
ageadult
cell typeHMDM
cell linePrimary
companyNA
collaborationBaillie/Tomoiu/Fisher/Hume
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
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-penis0.119
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.177
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.274
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs13650

Jaspar motifP-value
MA0002.24.70481e-4
MA0003.10.126
MA0004.10.202
MA0006.10.683
MA0007.10.0759
MA0009.10.273
MA0014.10.233
MA0017.10.00198
MA0018.20.005
MA0019.10.575
MA0024.10.00733
MA0025.10.449
MA0027.10.142
MA0028.10.454
MA0029.10.683
MA0030.10.00583
MA0031.10.114
MA0035.20.721
MA0038.10.0382
MA0039.20.927
MA0040.10.804
MA0041.10.441
MA0042.10.822
MA0043.10.0143
MA0046.10.184
MA0047.20.434
MA0048.10.432
MA0050.12.02255e-4
MA0051.10.00941
MA0052.10.23
MA0055.10.646
MA0057.10.596
MA0058.10.0462
MA0059.10.133
MA0060.13.96578e-9
MA0061.10.124
MA0062.20.613
MA0065.20.00234
MA0066.10.00285
MA0067.10.285
MA0068.19.30148e-4
MA0069.10.717
MA0070.10.739
MA0071.10.0709
MA0072.10.856
MA0073.10.367
MA0074.10.151
MA0076.10.253
MA0077.10.467
MA0078.10.796
MA0079.20.927
MA0080.25.47982e-15
MA0081.10.00155
MA0083.10.278
MA0084.10.329
MA0087.10.82
MA0088.10.504
MA0090.10.0146
MA0091.10.197
MA0092.10.29
MA0093.10.184
MA0099.20.446
MA0100.10.592
MA0101.10.698
MA0102.20.0299
MA0103.10.291
MA0104.20.369
MA0105.17.49777e-4
MA0106.10.969
MA0107.10.625
MA0108.21.65305e-5
MA0111.10.215
MA0112.22.75626e-5
MA0113.10.507
MA0114.10.0146
MA0115.10.44
MA0116.17.22934e-5
MA0117.10.734
MA0119.10.517
MA0122.10.991
MA0124.10.454
MA0125.10.971
MA0131.10.213
MA0135.10.609
MA0136.13.07627e-9
MA0137.20.965
MA0138.20.275
MA0139.10.24
MA0140.10.417
MA0141.10.00915
MA0142.10.116
MA0143.10.0935
MA0144.10.262
MA0145.10.118
MA0146.10.0492
MA0147.10.483
MA0148.10.87
MA0149.10.00861
MA0150.10.158
MA0152.10.754
MA0153.10.0169
MA0154.10.00337
MA0155.10.531
MA0156.10.0132
MA0157.10.894
MA0159.10.00422
MA0160.10.0152
MA0162.10.289
MA0163.12.74904e-9
MA0164.10.99
MA0258.17.73808e-4
MA0259.10.822



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: CNhs13650

Novel motifP-value
10.0794
100.0319
1000.826
1010.246
1020.633
1030.0708
1040.764
1050.671
1060.017
1070.29
1080.635
1090.054
110.0432
1100.221
1110.0098
1120.029
1130.976
1140.00388
1150.825
1160.566
1170.09
1180.297
1190.0819
120.767
1200.163
1210.411
1220.958
1230.102
1240.396
1250.0187
1260.328
1270.132
1280.0281
1290.377
130.08
1300.402
1310.899
1320.548
1330.418
1340.609
1350.0476
1360.973
1370.0759
1380.299
1390.0271
140.44
1400.114
1410.49
1420.639
1430.0986
1440.349
1450.29
1460.778
1470.513
1480.00982
1490.379
150.127
1500.454
1510.524
1520.143
1530.652
1540.951
1550.161
1560.83
1570.859
1580.65
1590.332
160.151
1600.201
1610.429
1620.902
1630.458
1640.0973
1650.354
1660.698
1670.0374
1680.546
1690.00343
170.206
180.134
190.216
20.841
200.949
210.351
220.2
230.23
240.186
250.467
260.0552
270.106
280.932
290.13
30.0422
300.662
310.515
320.216
330.307
340.364
350.256
360.037
370.0901
380.128
390.645
40.718
400.0796
410.139
420.599
430.11
440.00895
450.604
460.0796
470.218
480.192
490.16
50.374
500.926
510.337
520.304
530.479
540.316
550.245
560.675
570.401
580.23
590.095
60.372
600.0528
610.195
620.135
630.283
640.166
650.0872
660.847
670.087
680.944
690.46
70.212
700.0168
710.0477
720.211
730.0499
740.765
750.0438
760.352
770.214
780.0765
790.0169
80.0519
800.868
810.164
820.0462
830.81
840.771
850.0028
860.0824
870.136
880.506
890.0819
90.366
900.0127
910.357
920.0712
930.627
940.0133
950.0953
960.124
970.95
980.124
990.621



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: CNhs13650


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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000235 (macrophage)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
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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