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FF:13311-142I8: 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, donor4 (227_121: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-penis0.441
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.366
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.235
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13639

Jaspar motifP-value
MA0002.20.00296
MA0003.10.168
MA0004.10.648
MA0006.10.721
MA0007.10.199
MA0009.10.0994
MA0014.10.739
MA0017.10.0275
MA0018.26.6275e-4
MA0019.10.207
MA0024.10.0263
MA0025.10.00541
MA0027.10.479
MA0028.10.0566
MA0029.10.55
MA0030.19.19678e-4
MA0031.10.165
MA0035.20.443
MA0038.10.00506
MA0039.20.275
MA0040.10.954
MA0041.10.0668
MA0042.10.244
MA0043.19.48741e-5
MA0046.10.0317
MA0047.20.816
MA0048.10.979
MA0050.10.515
MA0051.10.94
MA0052.10.0356
MA0055.10.795
MA0057.10.707
MA0058.10.5
MA0059.10.145
MA0060.12.87353e-9
MA0061.10.124
MA0062.20.0703
MA0065.20.00272
MA0066.10.0132
MA0067.10.763
MA0068.11.48602e-4
MA0069.10.894
MA0070.10.318
MA0071.10.0975
MA0072.10.701
MA0073.10.507
MA0074.10.193
MA0076.10.014
MA0077.10.527
MA0078.10.976
MA0079.20.165
MA0080.26.29503e-6
MA0081.10.0567
MA0083.10.899
MA0084.10.221
MA0087.10.709
MA0088.10.429
MA0090.10.258
MA0091.10.0991
MA0092.10.178
MA0093.10.685
MA0099.20.88
MA0100.10.472
MA0101.10.951
MA0102.20.497
MA0103.10.159
MA0104.20.515
MA0105.11.66128e-5
MA0106.10.609
MA0107.10.849
MA0108.21.12156e-5
MA0111.10.33
MA0112.22.83741e-5
MA0113.10.601
MA0114.10.0472
MA0115.10.642
MA0116.14.00956e-5
MA0117.10.938
MA0119.10.213
MA0122.10.645
MA0124.10.221
MA0125.10.382
MA0131.10.251
MA0135.10.425
MA0136.10.133
MA0137.20.0403
MA0138.20.106
MA0139.10.212
MA0140.10.415
MA0141.10.028
MA0142.10.115
MA0143.10.19
MA0144.10.709
MA0145.10.265
MA0146.10.185
MA0147.10.411
MA0148.10.71
MA0149.10.0225
MA0150.10.418
MA0152.10.868
MA0153.10.0468
MA0154.10.00347
MA0155.10.592
MA0156.10.716
MA0157.10.933
MA0159.10.00581
MA0160.10.0997
MA0162.10.326
MA0163.11.56635e-11
MA0164.10.813
MA0258.10.0018
MA0259.10.859



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: CNhs13639

Novel motifP-value
10.0333
100.0272
1000.576
1010.253
1020.792
1030.0864
1040.686
1050.901
1060.0154
1070.0672
1080.432
1090.131
110.0639
1100.108
1110.00135
1120.0227
1130.874
1140.00282
1150.458
1160.424
1170.121
1180.317
1190.0306
120.911
1200.863
1210.286
1220.579
1230.077
1240.306
1250.0143
1260.539
1270.219
1280.0415
1290.345
130.129
1300.135
1310.494
1320.806
1330.552
1340.777
1350.19
1360.908
1370.0994
1380.542
1390.0279
140.574
1400.0872
1410.439
1420.767
1430.184
1440.371
1450.125
1460.792
1470.899
1480.00577
1490.213
150.072
1500.475
1510.438
1520.325
1530.835
1540.69
1550.13
1560.651
1570.584
1580.474
1590.804
160.135
1600.0935
1610.406
1620.387
1630.809
1640.217
1650.116
1660.807
1670.0267
1680.507
1690.004
170.138
180.0991
190.149
20.855
200.839
210.262
220.295
230.169
240.485
250.703
260.0156
270.232
280.874
290.288
30.054
300.459
310.595
320.128
330.396
340.648
350.115
360.0317
370.133
380.207
390.426
40.743
400.243
410.485
420.527
430.0882
440.0231
450.821
460.0371
470.175
480.223
490.131
50.379
500.99
510.447
520.374
530.614
540.43
550.161
560.553
570.212
580.235
590.118
60.293
600.0894
610.356
620.0924
630.207
640.18
650.0914
660.65
670.234
680.721
690.353
70.414
700.00913
710.0448
720.325
730.209
740.517
750.111
760.451
770.171
780.148
790.00175
80.0356
800.781
810.138
820.0841
830.989
840.771
850.00586
860.225
870.652
880.774
890.0495
90.439
900.054
910.373
920.0829
930.396
940.0245
950.267
960.076
970.994
980.116
990.978



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: CNhs13639


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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