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FF:13317-143A5: 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, donor2 (150_120: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-penis0.0872
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-0.394
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13646

Jaspar motifP-value
MA0002.23.71377e-4
MA0003.10.125
MA0004.10.211
MA0006.10.618
MA0007.10.143
MA0009.10.165
MA0014.10.539
MA0017.10.00474
MA0018.20.016
MA0019.10.406
MA0024.10.00929
MA0025.10.77
MA0027.10.542
MA0028.10.114
MA0029.10.805
MA0030.10.00848
MA0031.10.23
MA0035.20.982
MA0038.10.0342
MA0039.20.913
MA0040.10.953
MA0041.10.821
MA0042.10.509
MA0043.10.033
MA0046.10.384
MA0047.20.568
MA0048.10.461
MA0050.14.0256e-5
MA0051.10.00297
MA0052.10.702
MA0055.10.807
MA0057.10.441
MA0058.10.0647
MA0059.10.0867
MA0060.12.53478e-8
MA0061.10.00979
MA0062.20.376
MA0065.20.00185
MA0066.10.00606
MA0067.10.338
MA0068.10.00242
MA0069.10.559
MA0070.10.267
MA0071.10.111
MA0072.10.53
MA0073.10.269
MA0074.10.142
MA0076.10.0589
MA0077.10.736
MA0078.10.771
MA0079.20.727
MA0080.25.32743e-14
MA0081.10.00388
MA0083.10.706
MA0084.10.15
MA0087.10.504
MA0088.10.707
MA0090.10.136
MA0091.10.14
MA0092.10.243
MA0093.10.206
MA0099.20.0689
MA0100.10.341
MA0101.10.0918
MA0102.20.0235
MA0103.10.217
MA0104.20.316
MA0105.16.96406e-5
MA0106.10.659
MA0107.10.0321
MA0108.20.058
MA0111.10.395
MA0112.22.87431e-5
MA0113.10.208
MA0114.10.0288
MA0115.10.358
MA0116.11.98288e-4
MA0117.10.87
MA0119.10.288
MA0122.10.711
MA0124.10.487
MA0125.10.727
MA0131.10.269
MA0135.10.584
MA0136.11.77376e-7
MA0137.20.574
MA0138.20.232
MA0139.10.314
MA0140.10.874
MA0141.10.0185
MA0142.10.042
MA0143.10.0533
MA0144.10.403
MA0145.10.115
MA0146.10.0875
MA0147.10.428
MA0148.10.816
MA0149.10.0164
MA0150.10.0906
MA0152.10.758
MA0153.10.0415
MA0154.10.00245
MA0155.10.381
MA0156.10.105
MA0157.10.763
MA0159.10.00379
MA0160.10.0406
MA0162.10.338
MA0163.11.4025e-7
MA0164.10.916
MA0258.10.00146
MA0259.10.752



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: CNhs13646

Novel motifP-value
10.082
100.0711
1000.774
1010.349
1020.848
1030.0676
1040.965
1050.378
1060.00569
1070.0917
1080.634
1090.0741
110.0545
1100.117
1110.00398
1120.0297
1130.917
1140.00808
1150.721
1160.532
1170.186
1180.38
1190.035
120.852
1200.201
1210.516
1220.906
1230.226
1240.25
1250.124
1260.307
1270.099
1280.0162
1290.168
130.104
1300.731
1310.831
1320.647
1330.978
1340.64
1350.0368
1360.81
1370.152
1380.378
1390.034
140.448
1400.0267
1410.542
1420.851
1430.0617
1440.506
1450.184
1460.788
1470.844
1480.0161
1490.131
150.0882
1500.464
1510.517
1520.153
1530.8
1540.913
1550.157
1560.86
1570.753
1580.602
1590.377
160.168
1600.0644
1610.279
1620.778
1630.908
1640.205
1650.324
1660.951
1670.226
1680.582
1690.00541
170.107
180.131
190.161
20.693
200.982
210.461
220.232
230.165
240.226
250.569
260.0214
270.152
280.804
290.199
30.0817
300.841
310.533
320.111
330.398
340.377
350.305
360.0278
370.101
380.152
390.469
40.718
400.0674
410.129
420.587
430.0992
440.0225
450.526
460.0809
470.234
480.242
490.137
50.326
500.91
510.304
520.273
530.488
540.309
550.116
560.576
570.316
580.296
590.0598
60.513
600.0462
610.292
620.163
630.23
640.228
650.0606
660.797
670.176
680.583
690.28
70.228
700.00843
710.0445
720.239
730.0987
740.691
750.0954
760.643
770.129
780.12
790.054
80.0603
800.623
810.181
820.0347
830.342
840.779
850.00695
860.209
870.203
880.63
890.0733
90.313
900.0445
910.468
920.107
930.487
940.0173
950.154
960.0858
970.782
980.0778
990.737



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: CNhs13646


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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