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FF:11888-125D7: 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 17:35, 29 March 2012


Name:CD14+ monocytes - treated with Candida, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
age21
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD5-9
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-Peripheral0.96
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-penis-0.168
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.372
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: CNhs13494

Jaspar motifP-value
MA0002.23.08947e-8
MA0003.10.755
MA0004.10.0566
MA0006.10.712
MA0007.10.748
MA0009.10.4
MA0014.10.586
MA0017.10.188
MA0018.20.0297
MA0019.10.857
MA0024.10.00744
MA0025.18.51557e-5
MA0027.10.795
MA0028.10.116
MA0029.10.125
MA0030.10.503
MA0031.10.52
MA0035.20.351
MA0038.10.866
MA0039.20.984
MA0040.10.545
MA0041.10.777
MA0042.10.644
MA0043.12.51655e-8
MA0046.10.00713
MA0047.20.341
MA0048.10.611
MA0050.13.29182e-7
MA0051.10.00623
MA0052.19.27135e-4
MA0055.10.403
MA0057.10.412
MA0058.10.00769
MA0059.10.0328
MA0060.12.55929e-5
MA0061.11.09085e-13
MA0062.20.712
MA0065.20.031
MA0066.10.0256
MA0067.16.78876e-7
MA0068.10.984
MA0069.10.819
MA0070.10.0202
MA0071.10.392
MA0072.10.529
MA0073.10.396
MA0074.10.111
MA0076.10.132
MA0077.10.399
MA0078.10.435
MA0079.20.145
MA0080.22.81737e-11
MA0081.10.0011
MA0083.10.652
MA0084.10.718
MA0087.10.675
MA0088.10.572
MA0090.10.551
MA0091.10.644
MA0092.10.479
MA0093.10.0647
MA0099.22.68876e-43
MA0100.10.863
MA0101.17.29839e-16
MA0102.21.31884e-7
MA0103.10.118
MA0104.20.0714
MA0105.15.71237e-19
MA0106.10.904
MA0107.14.88551e-19
MA0108.20.895
MA0111.10.467
MA0112.21.43369e-4
MA0113.10.998
MA0114.10.252
MA0115.10.692
MA0116.10.00128
MA0117.10.0405
MA0119.10.132
MA0122.10.607
MA0124.10.237
MA0125.10.212
MA0131.10.392
MA0135.10.541
MA0136.15.77732e-13
MA0137.20.278
MA0138.20.404
MA0139.10.871
MA0140.10.541
MA0141.10.133
MA0142.10.661
MA0143.10.925
MA0144.10.135
MA0145.10.552
MA0146.10.568
MA0147.10.138
MA0148.10.771
MA0149.10.146
MA0150.13.23094e-20
MA0152.10.904
MA0153.10.00592
MA0154.12.68983e-4
MA0155.10.882
MA0156.14.30772e-8
MA0157.10.915
MA0159.10.0363
MA0160.10.027
MA0162.10.886
MA0163.11.11757e-7
MA0164.10.675
MA0258.10.0164
MA0259.10.864



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: CNhs13494

Novel motifP-value
10.117
100.0241
1000.915
1010.773
1020.971
1030.29
1040.484
1050.0736
1060.00117
1070.28
1080.804
1090.37
110.214
1100.16
1110.106
1120.38
1130.543
1140.0417
1150.256
1160.959
1170.0735
1180.182
1190.133
120.284
1200.655
1210.573
1220.509
1230.597
1240.671
1250.411
1260.184
1270.52
1280.045
1290.403
130.0779
1300.334
1310.951
1320.0442
1330.661
1340.69
1350.96
1360.998
1370.04
1380.387
1390.0581
140.557
1400.309
1410.328
1420.0247
1430.0243
1440.74
1450.399
1460.876
1470.87
1480.0189
1490.952
150.183
1500.359
1510.46
1520.398
1530.623
1540.786
1550.893
1560.527
1570.423
1580.0191
1590.191
160.323
1600.353
1610.488
1620.313
1630.123
1640.137
1650.401
1660.676
1670.197
1680.271
1690.0163
170.263
180.118
190.536
20.467
200.211
210.775
220.361
230.0433
240.435
250.42
260.0969
270.511
280.42
290.277
30.18
300.545
310.765
320.533
330.222
340.807
350.109
360.0716
370.0654
380.346
390.82
40.826
400.16
410.00995
420.422
430.0219
440.556
450.807
460.232
470.705
480.599
490.12
50.31
500.968
510.555
520.48
530.665
540.468
550.742
560.704
570.925
580.183
590.245
60.869
600.0697
610.773
620.101
630.574
640.414
650.218
660.416
670.52
680.663
690.405
70.197
700.0888
710.0305
720.227
730.198
740.124
750.122
760.168
770.497
780.12
790.486
80.375
800.186
810.351
820.357
830.00334
840.134
850.0519
860.0558
870.535
880.81
890.274
90.455
900.136
910.306
920.414
930.429
940.101
950.466
960.385
970.52
980.14
990.0506



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: CNhs13494


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)
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)
0000860 (classical monocyte)
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)
0002057 (CD14-positive, CD16-negative classical monocyte)
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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