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FF:11866-125B3: 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 17:32, 29 March 2012


Name:CD14+ monocytes - treated with Salmonella, donor1
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
age69
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD3-7
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-Peripheral0.885
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
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
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-Whole0.199
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: CNhs13471

Jaspar motifP-value
MA0002.21.91395e-6
MA0003.10.612
MA0004.10.704
MA0006.10.882
MA0007.10.818
MA0009.10.262
MA0014.10.973
MA0017.10.153
MA0018.20.286
MA0019.10.349
MA0024.10.00248
MA0025.10.0183
MA0027.10.936
MA0028.10.095
MA0029.10.112
MA0030.10.0567
MA0031.10.229
MA0035.20.188
MA0038.10.189
MA0039.20.501
MA0040.10.681
MA0041.10.882
MA0042.10.575
MA0043.17.22744e-7
MA0046.10.0082
MA0047.20.217
MA0048.10.561
MA0050.16.47694e-17
MA0051.11.16649e-11
MA0052.10.713
MA0055.10.471
MA0057.10.437
MA0058.10.529
MA0059.10.3
MA0060.14.51088e-12
MA0061.15.77749e-15
MA0062.20.837
MA0065.20.0211
MA0066.10.0344
MA0067.13.58724e-4
MA0068.10.121
MA0069.10.905
MA0070.10.0174
MA0071.10.411
MA0072.10.853
MA0073.10.564
MA0074.10.111
MA0076.10.0841
MA0077.10.321
MA0078.10.578
MA0079.20.17
MA0080.21.33287e-11
MA0081.16.94572e-4
MA0083.10.665
MA0084.10.563
MA0087.10.966
MA0088.10.401
MA0090.10.466
MA0091.10.651
MA0092.10.304
MA0093.10.781
MA0099.22.90136e-41
MA0100.10.675
MA0101.13.21509e-18
MA0102.27.2988e-10
MA0103.10.121
MA0104.20.771
MA0105.13.13504e-18
MA0106.10.992
MA0107.12.86424e-23
MA0108.20.0694
MA0111.10.45
MA0112.21.77291e-4
MA0113.10.704
MA0114.10.141
MA0115.10.952
MA0116.12.76495e-4
MA0117.10.133
MA0119.10.1
MA0122.10.777
MA0124.10.571
MA0125.10.221
MA0131.10.422
MA0135.10.276
MA0136.14.73401e-11
MA0137.20.225
MA0138.20.622
MA0139.10.801
MA0140.10.19
MA0141.10.111
MA0142.10.698
MA0143.10.95
MA0144.10.0929
MA0145.10.47
MA0146.10.317
MA0147.10.788
MA0148.10.516
MA0149.10.195
MA0150.14.31463e-19
MA0152.10.811
MA0153.18.61476e-4
MA0154.15.61635e-4
MA0155.10.92
MA0156.18.44835e-7
MA0157.10.843
MA0159.10.0278
MA0160.10.131
MA0162.10.682
MA0163.12.57327e-9
MA0164.10.465
MA0258.10.0128
MA0259.10.532



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: CNhs13471

Novel motifP-value
10.0839
100.0237
1000.998
1010.963
1020.972
1030.198
1040.541
1050.198
1064.01834e-4
1070.139
1080.813
1090.288
110.12
1100.171
1110.0367
1120.352
1130.429
1140.0149
1150.246
1160.825
1170.0674
1180.165
1190.122
120.275
1200.963
1210.82
1220.892
1230.386
1240.729
1250.152
1260.213
1270.497
1280.0483
1290.32
130.102
1300.16
1310.881
1320.148
1330.512
1340.335
1350.734
1360.996
1370.0426
1380.316
1390.0633
140.495
1400.352
1410.233
1420.221
1430.0253
1440.537
1450.282
1460.722
1470.958
1480.00621
1490.766
150.153
1500.319
1510.482
1520.307
1530.723
1540.744
1550.787
1560.806
1570.479
1580.0487
1590.401
160.286
1600.346
1610.413
1620.339
1630.0683
1640.084
1650.166
1660.925
1670.223
1680.109
1690.0116
170.172
180.0846
190.415
20.58
200.16
210.705
220.313
230.0265
240.442
250.546
260.0447
270.603
280.36
290.237
30.0817
300.354
310.69
320.82
330.207
340.664
350.1
360.073
370.0699
380.38
390.72
40.943
400.25
410.0259
420.264
430.0214
440.697
450.742
460.134
470.432
480.413
490.124
50.314
500.986
510.468
520.299
530.575
540.397
550.519
560.622
570.719
580.181
590.161
60.688
600.0342
610.738
620.0859
630.435
640.495
650.188
660.199
670.452
680.548
690.247
70.266
700.0315
710.0281
720.244
730.207
740.0339
750.155
760.146
770.412
780.103
790.63
80.297
800.282
810.305
820.114
830.0783
840.064
850.0188
860.0819
870.667
880.79
890.166
90.299
900.0731
910.318
920.227
930.66
940.0746
950.405
960.343
970.529
980.108
990.114



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: CNhs13471


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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