FF:3632-171A1: Difference between revisions

Latest revision as of 19:12, 4 June 2020

Name:	macrophage, bone marrow derived
Species:	Mouse (Mus musculus)
Library ID:	CNhs11532
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	BALB/c
tissue	bone marrow
dev stage	UNDEFINED_DEV_STAGE
sex	male
age	NA
cell type	macrophage
cell line	NA
company	NA
collaboration	Frank Brombacher (University of Cape Town, South Africa)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	total RNA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005999

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11532		CAGE		DRX008915		DRR009789

Accession ID Mm9

Library id		BAM		CTSS
CNhs11532		DRZ001214		DRZ002597

Accession ID Mm10

Library id		BAM		CTSS
CNhs11532		DRZ012564		DRZ013947

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	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. Analyst:NA link to dataset. data

CNhs11532

0	0
1	0
10	0
100	0
1000	0
1001	0.055
1002	-0.116
1003	-0.123
1004	0
1005	0
1006	-0.143
1007	-0.277
1008	0
1009	-0.19
101	-0.0725
1010	0
1011	-0.0175
1012	0
1013	-0.0281
1014	-0.0874
1015	-0.267
1016	-0.465
1017	0
1018	0
1019	0
102	0
1020	0.42
1021	0.0839
1022	-0.315
1023	0
1024	-0.241
1025	-0.0611
1026	0
1027	0
1028	0
1029	-0.0989
103	-0.0887
1030	0
1031	-0.873
1032	-0.184
1033	0
1034	0
1035	0
1036	-0.158
1037	0
1038	0.0361
1039	-0.0849
104	0
1040	-0.809
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs11532

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.18394e-5
MA0003.1	MA0003.1	0.392
MA0004.1	MA0004.1	0.243
MA0006.1	MA0006.1	0.509
MA0007.1	MA0007.1	0.594
MA0009.1	MA0009.1	0.192
MA0014.1	MA0014.1	0.493
MA0017.1	MA0017.1	0.0566
MA0018.2	MA0018.2	0.0181
MA0019.1	MA0019.1	0.629
MA0024.1	MA0024.1	0.0511
MA0025.1	MA0025.1	0.99
MA0027.1	MA0027.1	0.665
MA0028.1	MA0028.1	0.0345
MA0029.1	MA0029.1	0.804
MA0030.1	MA0030.1	0.139
MA0031.1	MA0031.1	0.457
MA0035.2	MA0035.2	0.134
MA0038.1	MA0038.1	0.00399
MA0039.2	MA0039.2	0.707
MA0040.1	MA0040.1	0.437
MA0041.1	MA0041.1	0.0918
MA0042.1	MA0042.1	0.66
MA0043.1	MA0043.1	0.178
MA0046.1	MA0046.1	6.38582e-11
MA0047.2	MA0047.2	0.377
MA0048.1	MA0048.1	0.482
MA0050.1	MA0050.1	2.17068e-24
MA0051.1	MA0051.1	1.62823e-17
MA0052.1	MA0052.1	1.95666e-4
MA0055.1	MA0055.1	0.583
MA0057.1	MA0057.1	0.698
MA0058.1	MA0058.1	0.0881
MA0059.1	MA0059.1	0.0553
MA0060.1	MA0060.1	6.76966e-12
MA0061.1	MA0061.1	0.00167
MA0062.2	MA0062.2	6.96372e-6
MA0065.2	MA0065.2	0.0242
MA0066.1	MA0066.1	0.00903
MA0067.1	MA0067.1	0.436
MA0068.1	MA0068.1	0.626
MA0069.1	MA0069.1	0.936
MA0070.1	MA0070.1	0.0595
MA0071.1	MA0071.1	0.299
MA0072.1	MA0072.1	0.374
MA0073.1	MA0073.1	0.893
MA0074.1	MA0074.1	0.138
MA0076.1	MA0076.1	0.0977
MA0077.1	MA0077.1	0.2
MA0078.1	MA0078.1	0.895
MA0079.2	MA0079.2	0.173
MA0080.2	MA0080.2	9.78586e-13
MA0081.1	MA0081.1	0.00255
MA0083.1	MA0083.1	0.00374
MA0084.1	MA0084.1	0.345
MA0087.1	MA0087.1	0.849
MA0088.1	MA0088.1	0.197
MA0090.1	MA0090.1	0.0438
MA0091.1	MA0091.1	0.341
MA0092.1	MA0092.1	0.618
MA0093.1	MA0093.1	0.217
MA0099.2	MA0099.2	0.00299
MA0100.1	MA0100.1	0.409
MA0101.1	MA0101.1	0.00152
MA0102.2	MA0102.2	0.0147
MA0103.1	MA0103.1	0.829
MA0104.2	MA0104.2	0.728
MA0105.1	MA0105.1	2.79239e-4
MA0106.1	MA0106.1	0.151
MA0107.1	MA0107.1	0.00106
MA0108.2	MA0108.2	3.45002e-9
MA0111.1	MA0111.1	0.378
MA0112.2	MA0112.2	7.75125e-5
MA0113.1	MA0113.1	0.477
MA0114.1	MA0114.1	0.194
MA0115.1	MA0115.1	0.441
MA0116.1	MA0116.1	0.0016
MA0117.1	MA0117.1	0.877
MA0119.1	MA0119.1	0.321
MA0122.1	MA0122.1	0.212
MA0124.1	MA0124.1	0.869
MA0125.1	MA0125.1	0.0792
MA0131.1	MA0131.1	0.777
MA0135.1	MA0135.1	0.00157
MA0136.1	MA0136.1	3.10862e-15
MA0137.2	MA0137.2	0.162
MA0138.2	MA0138.2	0.769
MA0139.1	MA0139.1	0.24
MA0140.1	MA0140.1	0.135
MA0141.1	MA0141.1	0.0603
MA0142.1	MA0142.1	0.685
MA0143.1	MA0143.1	0.0861
MA0144.1	MA0144.1	0.368
MA0145.1	MA0145.1	0.165
MA0146.1	MA0146.1	0.00856
MA0147.1	MA0147.1	0.716
MA0148.1	MA0148.1	0.626
MA0149.1	MA0149.1	0.107
MA0150.1	MA0150.1	0.00916
MA0152.1	MA0152.1	0.75
MA0153.1	MA0153.1	1.94603e-6
MA0154.1	MA0154.1	0.0151
MA0155.1	MA0155.1	0.853
MA0156.1	MA0156.1	1.04402e-9
MA0157.1	MA0157.1	0.644
MA0159.1	MA0159.1	0.00106
MA0160.1	MA0160.1	0.209
MA0162.1	MA0162.1	0.273
MA0163.1	MA0163.1	3.34615e-5
MA0164.1	MA0164.1	0.9
MA0258.1	MA0258.1	0.00475
MA0259.1	MA0259.1	0.775

FANTOM5 phase1 novel unique motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs11532

Novel motif	Logo	P-value
1	1	0.039
10	10	0.0233
100	100	0.947
101	101	0.824
102	102	0.571
103	103	0.0251
104	104	0.892
105	105	0.843
106	106	0.101
107	107	0.487
108	108	0.826
109	109	0.0345
11	11	0.0604
110	110	0.0493
111	111	0.00274
112	112	0.00894
113	113	0.63
114	114	0.0126
115	115	0.675
116	116	0.522
117	117	6.5589e-4
118	118	0.263
119	119	0.175
12	12	0.823
120	120	0.174
121	121	0.183
122	122	0.673
123	123	0.675
124	124	0.764
125	125	0.179
126	126	0.292
127	127	0.45
128	128	0.0546
129	129	0.0758
13	13	0.0118
130	130	0.865
131	131	0.423
132	132	0.662
133	133	0.823
134	134	0.526
135	135	0.908
136	136	0.995
137	137	0.103
138	138	0.998
139	139	0.0546
14	14	0.843
140	140	0.047
141	141	0.088
142	142	0.606
143	143	0.0309
144	144	0.881
145	145	0.0737
146	146	0.708
147	147	0.678
148	148	0.0546
149	149	0.0927
15	15	0.0615
150	150	0.206
151	151	0.282
152	152	0.267
153	153	0.536
154	154	0.729
155	155	0.6
156	156	0.308
157	157	0.866
158	158	0.222
159	159	0.895
160	160	0.377
161	161	0.17
162	162	0.775
163	163	0.783
164	164	0.0689
165	165	0.0589
166	166	0.783
167	167	0.391
168	168	0.955
169	169	0.00335
17	17	0.126
18	18	0.175
19	19	0.159
2	2	0.575
20	20	0.116
21	21	0.51
22	22	0.224
23	23	0.667
24	24	0.281
25	25	0.311
26	26	0.00461
27	27	0.975
28	28	0.417
29	29	0.0549
3	3	0.0179
30	30	0.537
31	31	0.649
32	32	0.836
33	33	0.123
34	34	0.955
35	35	0.46
36	36	0.0247
37	37	0.0243
38	38	0.292
39	39	0.731
4	4	0.428
40	40	0.124
41	41	0.373
42	42	0.234
43	43	0.041
44	44	0.309
45	45	0.9
46	46	0.0593
47	47	0.112
48	48	0.204
49	49	0.0546
5	5	0.178
50	50	0.987
51	51	0.864
52	52	0.888
53	53	0.571
54	54	0.75
55	55	0.95
56	56	0.476
57	57	0.43
58	58	0.311
59	59	0.161
6	6	0.885
60	60	0.203
61	61	0.151
62	62	0.0996
63	63	0.313
64	64	0.574
65	65	0.263
66	66	0.519
67	67	0.104
68	68	0.00381
69	69	0.651
7	7	0.119
70	70	0.0054
71	71	0.0284
72	72	0.178
73	73	0.0279
74	74	0.831
75	75	0.012
76	76	0.0674
77	77	0.553
78	78	0.0843
79	79	0.549
8	8	0.0329
80	80	0.692
81	81	0.243
82	82	0.276
83	83	0.879
84	84	0.687
85	85	0.355
86	86	0.226
87	87	0.62
88	88	0.699
89	89	0.154
9	9	0.518
90	90	0.0348
91	91	0.553
92	92	0.093
93	93	0.118
94	94	0.279
95	95	0.0476
96	96	0.5
97	97	0.819
98	98	0.283
99	99	1

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown. Analyst:NA library id: CNhs11532

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
FF:0000103 mouse sample
FF:0200021 macrophage, bone marrow-derived sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0002476 (bone marrow macrophage)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0200021 (macrophage, bone marrow-derived sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000926,UBERON:0000479,UBERON:0000062,UBERON:0004765,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405,UBERON:0003081,UBERON:0006603,UBERON:0003061
+|DRA_sample_Accession=CAGE@SAMD00005999
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000839,CL:0000548,CL:0002194,CL:0000034,CL:0002032,CL:0000763,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000766,CL:0000219,CL:0000004,CL:0000134,CL:0000738,CL:0002087,CL:0000255,CL:0002031,CL:0000576,CL:0000235,CL:0000037,CL:0000566,CL:0000049,CL:0000557,CL:0000837,CL:0002009,CL:0000040,CL:0000559
+|accession_numbers=CAGE;DRX008915;DRR009789;DRZ001214;DRZ002597;DRZ012564;DRZ013947
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002371,UBERON:0001474,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000219,CL:0000325,CL:0000473,CL:0000234,CL:0000738,CL:0000255,CL:0000235,CL:0000864,CL:0002476
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001,FF:0200021
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor=pool2
 |expression_enrichment_score=chr7:148452314..148452329,-!p1@Irf7!2.32!1353.78!Irf7;;chr2:173044380..173044432,-!p1@Zbp1!2.21!373.12!Zbp1;;chr2:90922554..90922575,+!p4@Sfpi1!2.07!207.77!Sfpi1;;chr2:90936901..90936945,+!p1@Sfpi1!1.94!428.05!Sfpi1;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.91!100.62!Zbtb11;;chr2:173044357..173044377,-!p2@Zbp1!1.87!102.25!Zbp1;;chr2:90936947..90936977,+!p2@Sfpi1!1.77!111.50!Sfpi1;;chr2:90936978..90937023,+!p3@Sfpi1!1.72!95.18!Sfpi1;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!1.63!41.34!Sp140;;chr2:90922519..90922544,+!p6@Sfpi1!1.61!43.51!Sfpi1;;chr11:16908650..16908690,-!p1@Plek!1.55!203.96!Plek;;chr6:29476690..29476724,+!p1@Irf5!1.50!135.98!Irf5;;chr5:53981592..53981616,+!p3@Rbpj!1.50!56.57!Rbpj;;chr1:193007123..193007139,-!p1@Atf3!1.46!150.12!Atf3;;chr8:87225329..87225396,+!p1@Lyl1!1.45!98.99!Lyl1;;chr8:123260252..123260264,+!p1@Irf8!1.36!150.12!Irf8;;chr7:87170879..87170914,+!p2@Zfp710!1.36!50.04!Zfp710;;chr1:52176315..52176343,+!p1@Stat1!1.32!277.39!Stat1;;chr2:166885917..166885930,-!p9@Znfx1!1.31!19.58!Znfx1;;chr11:11586218..11586285,+!p1@Ikzf1!1.27!55.48!Ikzf1;;chrX:7339938..7339963,+!p1@Tfe3!1.25!84.31!Tfe3;;chr7:20408047..20408125,-!p1@Bcl3!1.24!182.21!Bcl3;;chr6:97757008..97757061,+!p1@Mitf!1.23!67.44!Mitf;;chr7:25917492..25917512,-!p1@Pou2f2!1.23!27.20!Pou2f2;;chr16:92826249..92826325,-!p1@Runx1!1.22!38.07!Runx1;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!1.18!16.86!Ncoa4;;chr6:145814003..145814056,-!p1@Bhlhe41!1.16!38.62!Bhlhe41;;chr2:166888107..166888224,-!p1@Znfx1!1.15!187.65!Znfx1;;chrX:7341077..7341091,+!p5@Tfe3!1.15!22.30!Tfe3;;chr2:160192793..160192809,-!p1@Mafb!1.14!191.45!Mafb;;chr11:53583544..53583559,+!p1@Irf1!1.13!205.60!Irf1;;chr6:39068181..39068206,-!p3@Parp12!1.13!25.56!Parp12;;chr2:166885947..166885956,-!p13@Znfx1!1.13!12.51!Znfx1;;chr2:90936886..90936898,+!p5@Sfpi1!1.10!13.60!Sfpi1;;chr16:3744162..3744180,+!p2@Zfp263!1.09!31.00!Zfp263;;chr6:39068163..39068176,-!p2@Parp12!1.08!20.67!Parp12;;chr10:127707602..127707633,+!p1@Stat2!1.07!96.27!Stat2;;chr2:91034924..91034946,-!p2@Nr1h3!1.06!13.05!Nr1h3;;chr2:167514456..167514473,+!p1@Cebpb!1.05!455.79!Cebpb;;chr2:44968512..44968530,-!p1@Zeb2!1.05!226.26!Zeb2;;chr2:166888058..166888105,-!p2@Znfx1!1.05!33.18!Znfx1;;chr6:145813905..145813932,-!p2@Bhlhe41!1.03!18.49!Bhlhe41;;chr16:3744192..3744206,+!p4@Zfp263!1.03!12.51!Zfp263;;chr7:20214704..20214800,-!p1@Relb!1.02!31.55!Relb;;chr6:29476741..29476752,+!p4@Irf5!1.02!10.33!Irf5;;chr7:26067619..26067702,+!p2@Cic!1.01!52.76!Cic;;chr17:71202822..71202877,-!p3@Tgif1!1.01!27.20!Tgif1;;chr4:124805092..124805135,-!p2@Zc3h12a!1.00!38.62!Zc3h12a;;chr11:100683839..100683890,-!p2@Stat5b!1.00!21.21!Stat5b;;chr2:91035197..91035237,-!p1@Nr1h3!1.00!19.04!Nr1h3;;chr19:46379199..46379301,+!p1@Nfkb2!0.99!51.67!Nfkb2;;chr1:87546583..87546595,+!p1@Sp100!0.99!12.51!Sp100;;chr6:53523358..53523388,+!p1@Creb5!0.97!101.71!Creb5;;chr5:53981578..53981590,+!p4@Rbpj!0.94!9.79!Rbpj;;chr7:25917459..25917474,-!p2@Pou2f2!0.94!7.61!Pou2f2;;chr4:53792566..53792578,+!p1@Tal2!0.94!7.61!Tal2;;chr8:118231705..118231722,-!p3@Maf!0.91!59.29!Maf;;chr8:87225670..87225697,+!p2@Lyl1!0.91!21.76!Lyl1;;chr15:50721515..50721540,-!p3@Trps1!0.91!21.76!Trps1;;chr6:98978868..98978918,-!p6@Foxp1!0.91!12.51!Foxp1;;chr16:92697560..92697592,-!p2@Runx1!0.90!45.69!Runx1;;chr9:32348943..32349001,-!p1@Fli1!0.89!58.20!Fli1;;chr1:87546602..87546617,+!p2@Sp100!0.89!8.16!Sp100;;chr1:186556410..186556424,-!p1@Hlx!0.88!21.76!Hlx;;chr6:29479277..29479296,+!p2@Irf5!0.88!6.53!Irf5;;chr16:15887371..15887385,+!p1@Cebpd!0.87!228.98!Cebpd;;chr13:37870307..37870337,+!p5@Rreb1!0.87!15.23!Rreb1;;chr12:78063057..78063070,-!p3@Max!0.87!14.14!Max;;chr17:27693887..27693908,+!p2@Hmga1-rs1,p2@Hmga1!0.84!45.14!Hmga1;;chr8:47825203..47825225,+!p3@Irf2!0.84!8.16!Irf2;;chr4:124805061..124805087,-!p1@Zc3h12a!0.83!19.04!Zc3h12a;;chr7:31206743..31206761,+!p1@Nfkbid!0.83!8.16!Nfkbid;;chr6:39068210..39068251,-!p1@Parp12!0.82!27.74!Parp12;;chr12:87027598..87027652,+!p1@Batf!0.82!13.60!Batf;;chr17:45692676..45692695,+!p2@Nfkbie!0.82!11.97!Nfkbie;;chr1:52176378..52176401,+!p3@Stat1!0.81!17.40!Stat1;;chrX:7339915..7339935,+!p4@Tfe3!0.81!13.05!Tfe3;;chr8:47825166..47825178,+!p2@Irf2!0.81!8.70!Irf2;;chr5:104121453..104121479,+!p4@Aff1!0.80!26.11!Aff1;;chr15:103170516..103170531,-!p2@Zfp385a!0.79!13.05!Zfp385a;;chr12:56593574..56593592,-!p1@Nfkbia!0.78!283.37!Nfkbia;;chr2:168415815..168415872,-!p1@Nfatc2!0.78!29.91!Nfatc2;;chr15:50721544..50721558,-!p5@Trps1!0.78!11.97!Trps1;;chr6:145813964..145813994,-!p3@Bhlhe41!0.78!6.53!Bhlhe41;;chr16:55838757..55838774,-!p2@Nfkbiz!0.78!5.98!Nfkbiz;;chr17:84587279..84587294,-!p1@Zfp36l2!0.77!567.29!Zfp36l2;;chr8:87502608..87502623,-!p1@Junb!0.77!87.02!Junb;;chr14:79915425..79915501,+!p1@Elf1!0.77!47.32!Elf1;;chr1:52176406..52176433,+!p2@Stat1!0.77!13.05!Stat1;;chr17:84586544..84586592,-!p3@Zfp36l2!0.77!7.07!Zfp36l2;;chr17:45692642..45692663,+!p1@Nfkbie!0.76!16.32!Nfkbie;;chr11:120491440..120491474,-!p3@Mafg!0.75!7.07!Mafg;;chr12:78063032..78063043,-!p4@Max!0.75!6.53!Max;;chr6:16848395..16848416,-!p2@Tfec!0.75!5.44!Tfec;;chr8:118231678..118231692,-!p2@Maf!0.74!45.14!Maf;;chr16:87699206..87699229,+!p3@Bach1!0.74!27.20!Bach1;;chr2:44965856..44965896,-!p5@Zeb2!0.74!19.04!Zeb2;;chr14:79915502..79915514,+!p4@Elf1!0.74!7.07!Elf1;;chr14:56223010..56223067,+!p1@Irf9!0.73!38.62!Irf9;;chr15:103170533..103170556,-!p1@Zfp385a!0.73!17.95!Zfp385a;;chr1:186556495..186556506,-!p8@Hlx!0.73!4.35!Hlx;;chr15:50721588..50721610,-!p1@Trps1!0.72!48.41!Trps1;;chr19:37509324..37509337,+!p1@Hhex!0.71!33.18!Hhex;;chr11:60036258..60036276,-!p3@Srebf1!0.71!7.61!Srebf1;;chr10:119913792..119913820,-!p5@Hmga2!0.71!7.61!Hmga2;;chr10:22451765..22451795,-!p6@Tbpl1!0.71!6.53!Tbpl1;;chr3:135354384..135354443,-!p1@Nfkb1!0.70!27.74!Nfkb1;;chr4:63064364..63064384,-!p1@Akna!0.70!13.05!Akna;;chr8:87225702..87225726,+!p3@Lyl1!0.70!8.70!Lyl1;;chr8:118231723..118231740,-!p1@Maf!0.69!99.53!Maf;;chr17:34784073..34784118,+!p2@Atf6b!0.69!17.40!Atf6b;;chr5:138187775..138187845,+!p7@Tsc22d4!0.68!5.44!Tsc22d4;;chr6:29479308..29479325,+!p3@Irf5!0.68!3.81!Irf5;;chr17:47906140..47906150,+!p6@Tfeb!0.68!3.81!Tfeb;;chr11:96685444..96685473,-!p5@Nfe2l1!0.68!3.81!Nfe2l1;;chr8:118230866..118230891,-!p4@Maf!0.67!27.74!Maf;;chr1:186556375..186556404,-!p3@Hlx!0.67!7.07!Hlx;;chr7:133838869..133838945,+!p2@Bola2!0.65!16.86!Bola2;;chr2:44968775..44968795,-!p4@Zeb2!0.63!17.95!Zeb2;;chr19:5637489..5637500,+!p5@Rela!0.63!9.25!Rela;;chr1:87546572..87546579,+!p4@Sp100!0.63!3.26!Sp100;;chr2:90936867..90936874,+!p7@Sfpi1!0.63!3.26!Sfpi1;;chr12:75002389..75002406,+!p4@Hif1a!0.63!3.26!Hif1a;;chr17:34784132..34784161,+!p1@Atf6b!0.62!21.21!Atf6b;;chr8:118230894..118230918,-!p5@Maf!0.62!10.33!Maf;;chr13:5860872..5860883,+!p3@Klf6!0.62!7.07!Klf6;;chr6:53523332..53523343,+!p2@Creb5!0.62!4.90!Creb5;;chr10:127080091..127080100,+!p4@Stat6!0.62!4.90!Stat6;;chr10:88145766..88145770,-!p1@Spic!0.62!4.35!Spic;;chr6:16848347..16848391,-!p1@Tfec!0.62!4.35!Tfec;;chr11:96690797..96690813,-!p1@Nfe2l1!0.61!70.16!Nfe2l1;;chr18:80904854..80904919,-!p2@Nfatc1!0.61!43.51!Nfatc1;;chr19:46380172..46380231,+!p2@Nfkb2!0.61!25.02!Nfkb2;;chr4:149943326..149943351,+!p4@Rere!0.61!6.53!Rere;;chr7:31207408..31207450,+!p4@Nfkbid!0.61!5.44!Nfkbid;;chr2:44965761..44965785,-!p13@Zeb2!0.61!4.90!Zeb2;;chr11:11590140..11590187,+!p3@Ikzf1!0.61!3.81!Ikzf1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.60!112.59!Nfkbiz;;chr3:30993974..30994045,+!p1@Skil!0.60!100.08!Skil;;chrX:103123886..103123922,-!p3@Atrx!0.60!9.25!Atrx;;chr2:165818125..165818167,+!p1@Ncoa3!0.59!94.10!Ncoa3;;chr13:5860776..5860796,+!p1@Klf6!0.59!86.48!Klf6;;chr8:111227738..111227793,+!p@chr8:111227738..111227793,+!0.59!8.16!Zfhx3;;chr16:92697354..92697362,-!p3@Runx1!0.59!4.90!Runx1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.57!34.81!Camta2;;chr2:153067079..153067090,-!p2@Plagl2!0.57!6.53!Plagl2;;chr8:118231350..118231385,-!p7@Maf!0.57!4.35!Maf;;chr19:6164433..6164446,+!p2@Batf2!0.57!2.72!Batf2;;chr11:70500401..70500460,-!p3@Camta2!0.57!2.72!Camta2;;chr12:87027663..87027678,+!p2@Batf!0.57!2.72!Batf;;chr19:46380235..46380277,+!p3@Nfkb2!0.56!6.53!Nfkb2;;chr7:52960555..52960662,+!p1@Dbp!0.55!27.20!Dbp;;chr19:5637501..5637517,+!p4@Rela!0.55!12.51!Rela;;chr3:135354375..135354381,-!p10@Nfkb1!0.55!3.26!Nfkb1;;chr10:67741461..67741483,-!p1@Arid5b!0.54!85.39!Arid5b;;chr10:127080031..127080090,+!p1@Stat6!0.54!67.44!Stat6;;chr16:3744146..3744157,+!p3@Zfp263!0.54!6.53!Zfp263;;chr4:114729646..114729665,+!p4@Tal1!0.54!3.81!Tal1;;chr11:74644437..74644507,+!p1@Mnt!0.53!80.50!Mnt;;chr11:11585678..11585745,+!p5@Ikzf1!0.53!3.81!Ikzf1;;chr7:31208285..31208312,+!p3@Nfkbid!0.53!2.72!Nfkbid;;chr7:133839456..133839523,+!p1@Bola2!0.52!150.66!Bola2;;chr1:36364590..36364608,+!p1@Arid5a!0.52!29.91!Arid5a;;chr14:19071466..19071550,-!p1@Nr1d2!0.52!20.12!Nr1d2;;chr19:5637528..5637548,+!p2@Rela!0.52!17.40!Rela;;chr5:104121391..104121450,+!p3@Aff1!0.52!15.23!Aff1;;chr16:17530781..17530882,-!p2@Thap7!0.51!16.86!Thap7;;chr15:76181718..76181729,+!p3@Maf1!0.51!6.53!Maf1;;chr17:71201096..71201114,-!p6@Tgif1!0.51!2.72!Tgif1;;chr8:72520139..72520157,-!p6@Gatad2a!0.50!10.88!Gatad2a;;chr17:84587167..84587239,-!p2@Zfp36l2!0.50!9.25!Zfp36l2;;chr10:80870405..80870428,-!p4@Nfic!0.50!7.07!Nfic;;chr11:11590117..11590138,+!p4@Ikzf1!0.50!2.18!Ikzf1;;chr16:92826232..92826245,-!p4@Runx1!0.50!2.18!Runx1;;chr6:29476684..29476685,+!p6@Irf5!0.50!2.18!Irf5;;chr7:52962498..52962512,+!p12@Dbp!0.50!2.18!Dbp;;chrX:137077653..137077669,-!p3@Tsc22d3!0.49!11.97!Tsc22d3;;chr13:37870253..37870272,+!p13@Rreb1!0.49!3.26!Rreb1;;chr14:79915521..79915539,+!p5@Elf1!0.49!2.72!Elf1;;chr15:80085920..80085941,+!p1@Atf4!0.48!313.29!Atf4;;chr2:75542527..75542590,-!p1@Nfe2l2!0.48!246.39!Nfe2l2;;chr10:126727842..126727859,+!p1@Ddit3!0.48!79.41!Ddit3;;chr5:142939972..142940026,+!p1@C330006K01Rik!0.48!35.90!C330006K01Rik;;chr13:44826722..44826742,+!p1@Jarid2!0.47!42.42!Jarid2;;chr8:72520121..72520135,-!p12@Gatad2a!0.47!4.90!Gatad2a;;chr10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10.88!L3mbtl2;;chr18:82862265..82862325,-!p1@Zfp236!0.04!8.70!Zfp236;;chr7:134169762..134169795,-!p3@Maz!0.04!8.16!Maz;;chr10:119913310..119913366,-!p1@Hmga2!0.04!7.07!Hmga2;;chr3:32409487..32409563,+!p1@Zfp639!0.04!6.53!Zfp639;;chr3:54611674..54611690,-!p2@Rfxap!0.04!6.53!Rfxap;;chr13:67585161..67585205,-!p1@Zfp874b!0.04!4.35!Zfp874b;;chr2:126501274..126501308,-!p2@Gabpb1!0.04!3.26!Gabpb1;;chr13:67274092..67274140,+!p1@Rsl1!0.04!2.72!Rsl1;;chr16:43363190..43363242,+!p2@Zbtb20!0.04!2.18!Zbtb20;;chr1:15795704..15795713,+!p2@Terf1!0.04!1.63!Terf1;;chr11:120494669..120494688,-!p2@Mafg!0.04!1.63!Mafg;;chr13:67229127..67229153,+!p2@Zfp759!0.04!1.09!Zfp759;;chr9:63869729..63869749,-!p4@Smad6!0.04!1.09!Smad6;;chr2:48805633..48805648,+!p5@Mbd5!0.04!1.09!Mbd5;;chr2:181100194..181100205,+!p5@Zgpat!0.04!1.09!Zgpat;;chrX:70587989..70588000,+!p3@Zfp275!0.04!1.09!Zfp275;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.04!1.09!Hmga1;;chr13:59924319..59924331,-!p5@Zcchc6!0.04!0.54!Zcchc6;;chr15:103170561..103170572,-!p4@Zfp385a!0.04!0.54!Zfp385a;;chr5:110539135..110539159,+!p4@Zfp605!0.04!0.54!Zfp605;;chr4:87679181..87679192,-!p10@Mllt3!0.04!0.54!Mllt3;;chr3:94668075..94668087,+!p6@Pogz!0.04!0.54!Pogz;;chr9:20385868..20385902,+!p3@Zfp846!0.04!0.54!Zfp846;;chr7:5003102..5003113,+!p4@Zfp580!0.04!0.54!Zfp580;;chr8:23970000..23970026,+!p1@Myst3!0.03!50.58!Myst3;;chr13:59924433..59924504,-!p1@Zcchc6!0.03!20.67!Zcchc6;;chr5:77694479..77694574,+!p1@Rest!0.03!20.12!Rest;;chr4:149943647..149943707,+!p2@Rere!0.03!16.86!Rere;;chrX:70587953..70587968,+!p1@Zfp275!0.03!9.79!Zfp275;;chr18:35721834..35721851,+!p2@Matr3!0.03!4.35!Matr3;;chr7:13466514..13466553,+!p1@Zfp128!0.03!3.81!Zfp128;;chr9:69137672..69137702,+!p2@Rora!0.03!3.26!Rora;;chr17:45570455..45570479,-!p2@Cdc5l!0.03!2.72!Cdc5l;;chr16:17531086..17531109,-!p3@Thap7!0.03!2.18!Thap7;;chrX:91368504..91368516,-!p3@Zfx!0.03!1.09!Zfx;;chrX:45947787..45947812,-!p3@Zfp280c!0.03!1.09!Zfp280c;;chr2:37286328..37286341,-!p3@Zbtb6!0.03!1.09!Zbtb6;;chr11:16952347..16952366,-!p2@Plek!0.03!0.54!Plek;;chr5:130175978..130175990,-!p2@Zfp11!0.03!0.54!Zfp11;;chr4:63071779..63071791,-!p3@Akna!0.03!0.54!Akna;;chr5:137043112..137043157,-!p1@Cux1!0.02!87.57!Cux1;;chr18:60720384..60720450,+!p1@Rbm22!0.02!48.95!Rbm22;;chr7:135056024..135056042,+!p1@Myst1!0.02!26.65!Myst1;;chr3:96001503..96001557,-!p1@Bola1!0.02!19.58!Bola1;;chr4:151363059..151363120,-!p1@Thap3!0.02!10.88!Thap3;;chr7:134170310..134170341,-!p5@Maz!0.02!7.61!Maz;;chr2:119698241..119698291,+!p2@Mga!0.02!3.81!Mga;;chr11:59285934..59285962,-!p1@Zfp867!0.02!2.72!Zfp867;;chr10:127984472..127984504,-!p2@Zc3h10!0.02!2.18!Zc3h10;;chr12:78063146..78063159,-!p2@Max!0.02!1.63!Max;;chr4:102792072..102792091,+!p5@Mier1!0.02!1.63!Mier1;;chr7:97591412..97591431,+!p2@Crebzf!0.02!1.63!Crebzf;;chr8:124900562..124900573,+!p3@Zc3h18!0.02!1.63!Zc3h18;;chr11:70501599..70501634,-!p2@Camta2,p2@LOC100048818!0.02!1.09!Camta2;;chr10:119913546..119913583,-!p3@Hmga2!0.02!1.09!Hmga2;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.02!0.54!Ppp1r13l;;chrX:103070746..103070764,-!p5@Atrx!0.02!0.54!Atrx;;chr1:13364153..13364156,-!p5@Ncoa2!0.02!0.54!Ncoa2;;chr6:99471223..99471254,-!p7@Foxp1!0.02!0.54!Foxp1;;chr18:69752912..69752928,+!p9@Tcf4!0.02!0.54!Tcf4;;chr16:55822638..55822669,-!p3@Nfkbiz!0.02!0.54!Nfkbiz;;chr14:65977415..65977426,+!p6@Zfp395!0.02!0.54!Zfp395;;chr12:3806513..3806527,+!p9@Dnmt3a!0.02!0.54!Dnmt3a;;chr8:125897678..125897746,+!p1@Tcf25!0.01!189.28!Tcf25;;chr15:81977668..81977705,+!p1@Srebf2!0.01!70.71!Srebf2;;chr5:108697948..108697999,+!p1@Dr1!0.01!28.28!Dr1;;chr4:118967105..118967123,-!p1@Ybx1!0.01!26.65!Ybx1;;chr6:86475924..86475935,-!p2@Pcbp1!0.01!14.69!Pcbp1;;chr2:28915759..28915807,+!p1@Ttf1!0.01!11.97!Ttf1;;chr11:4604645..4604705,+!p1@Zmat5!0.01!11.42!Zmat5;;chr3:14578609..14578687,+!p1@E2f5!0.01!8.16!E2f5;;chr3:94819136..94819168,-!p2@Zfp687!0.01!3.81!Zfp687;;chr2:181100154..181100181,+!p3@Zgpat!0.01!3.81!Zgpat;;chr13:44826095..44826185,+!p4@Jarid2!0.01!3.81!Jarid2;;chr11:69579472..69579529,+!p1@Zbtb4!0.01!3.81!Zbtb4;;chr7:135020060..135020124,-!p2@Zfp668!0.01!3.26!Zfp668;;chr4:108131994..108132056,+!p2@Zcchc11!0.01!2.18!Zcchc11;;chr4:135842030..135842065,+!p3@Zfp46!0.01!1.63!Zfp46;;chr6:133985971..133985991,+!p6@Etv6!0.01!1.63!Etv6;;chr1:64167550..64167618,-!p4@Klf7!0.01!1.63!Klf7;;chr2:181100223..181100237,+!p4@Zgpat!0.01!1.63!Zgpat;;chrX:7339829..7339855,+!p3@Tfe3!0.01!1.63!Tfe3;;chr6:99471044..99471066,-!p4@Foxp1!0.01!1.09!Foxp1;;chr15:75799598..75799619,+!p3@Zfp707!0.01!1.09!Zfp707;;chr15:75672367..75672384,-!p2@Zc3h3!0.01!1.09!Zc3h3;;chr14:98568532..98568561,-!p4@Dach1!0.01!0.54!Dach1;;chrX:7339674..7339688,+!p6@Tfe3!0.01!0.54!Tfe3;;chr4:133801432..133801448,-!p3@Zfp593!0.01!0.54!Zfp593;;chr3:51144477..51144506,-!p6@Elf2!0.01!0.54!Elf2;;chr3:103772552..103772584,+!p2@Phtf1!0.01!0.54!Phtf1;;chr19:23216132..23216157,+!p3@Klf9!0.01!0.54!Klf9;;chr15:80085678..80085693,+!p2@Atf4!0.01!0.54!Atf4;;chr19:55817590..55817625,+!p11@Tcf7l2!0.01!0.54!Tcf7l2;;chr5:6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+|ffid_belonging_in_development=CL:0000049,CL:0000134,UBERON:0002532,UBERON:0006603,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 37: / Line 44: @@
 |id=FF:3632-171A1
 |is_a=FF:0000103;;FF:0200021
-|name=macrophage, bone marrow derived, pool2
+|is_obsolete=
+|library_id=CNhs11532
+|library_id_phase_based=2:CNhs11532
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;3632
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;3632
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm9.nobarcode.rdna.fa.gz
+|name=macrophage, bone marrow derived
 |namespace=
 |part_of=
@@ Line 44: / Line 63: @@
 |profile_rnaseq=
 |profile_srnaseq=
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.273427585559424,0,0,0,0,-0.0843392403965415,0,0,0,0,0.094310383023109,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.319691257886324,0.62174747898574,0,0,0,0,0,0.160642500630131,-0.091558018055706,0.185127659736198,-0.984211366477826,-0.269868638010351,1.11280350661856,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.145773810963343,0,0.0472286190463524,0,0,0,-0.117389802908326,-0.310650657339386,-0.158091042771083,-0.0463773002441839,0,0.110612165294266,-0.102093492362586,0,0,0,-0.135257665540932,-0.0427582345239118,0.681668838148152,-0.0788315948399074,0,0,0,0,0,0,0.238091414570987,-0.044172402242288,0.618866726983152,0,0,0,0.47244086492021,0
 |rna_box=171
 |rna_catalog_number=
@@ Line 57: / Line 77: @@
 |rna_weight_ug=59.738
 |sample_age=
+|sample_category=time courses
 |sample_cell_catalog=
-|sample_cell_line=UNDEFINED_CELL_LINE
+|sample_cell_line=
 |sample_cell_lot=
 |sample_cell_type=macrophage
@@ Line 75: / Line 96: @@
 |sample_strain=BALB/c
 |sample_tissue=bone marrow
+|time=000hr
+|timecourse=BMM_TB_activation_IL4,BMM_TB_activation_IFNg,BMM_TB_activation_IL13,BMM_TB_activation_IL4-IL13
 |top_motifs=
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:3632-171A1;search_select_hide=table117:3632-171A1
 }}

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FF:3632-171A1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:12, 4 June 2020

CNhs11532

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0