FF:10260-104C8: Difference between revisions

Latest revision as of 13:57, 3 June 2020

Name:	Ileum epithelium, treated with RANKL, day03, pool3
Species:	Mouse (Mus musculus)
Library ID:	CNhs13234
Sample type:	tissues
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	Balb/c
tissue	ileum
dev stage	NA
sex	female
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	Shinji Fukuda (RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	R-3day_ileum_c
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005036

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13234		CAGE		DRX008919		DRR009793

Accession ID Mm9

Library id		BAM		CTSS
CNhs13234		DRZ001218		DRZ002601

Accession ID Mm10

Library id		BAM		CTSS
CNhs13234		DRZ012568		DRZ013951

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

CNhs13234

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0631
1002	-0.116
1003	-0.175
1004	0
1005	1.103
1006	-0.292
1007	-0.0978
1008	1.695
1009	-0.2
101	-0.0744
1010	0
1011	-0.298
1012	0
1013	0.46
1014	-0.0874
1015	-0.278
1016	-0.479
1017	0
1018	0.658
1019	0
102	0
1020	0
1021	0
1022	-0.0395
1023	0
1024	-0.237
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.0606
103	-0.0887
1030	0
1031	-0.685
1032	0.797
1033	0.087
1034	0
1035	0
1036	0.171
1037	0
1038	-0.136
1039	-0.0243
104	0.087
1040	-0.617
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: CNhs13234

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0045
MA0003.1	MA0003.1	0.2
MA0004.1	MA0004.1	0.639
MA0006.1	MA0006.1	0.134
MA0007.1	MA0007.1	0.212
MA0009.1	MA0009.1	0.128
MA0014.1	MA0014.1	0.136
MA0017.1	MA0017.1	6.60303e-17
MA0018.2	MA0018.2	0.56
MA0019.1	MA0019.1	0.231
MA0024.1	MA0024.1	0.236
MA0025.1	MA0025.1	0.167
MA0027.1	MA0027.1	0.941
MA0028.1	MA0028.1	0.00175
MA0029.1	MA0029.1	0.509
MA0030.1	MA0030.1	0.773
MA0031.1	MA0031.1	0.65
MA0035.2	MA0035.2	0.0027
MA0038.1	MA0038.1	0.739
MA0039.2	MA0039.2	8.73542e-5
MA0040.1	MA0040.1	0.0344
MA0041.1	MA0041.1	0.361
MA0042.1	MA0042.1	0.561
MA0043.1	MA0043.1	0.543
MA0046.1	MA0046.1	7.58674e-43
MA0047.2	MA0047.2	0.0317
MA0048.1	MA0048.1	0.301
MA0050.1	MA0050.1	5.57877e-5
MA0051.1	MA0051.1	6.54702e-5
MA0052.1	MA0052.1	0.00375
MA0055.1	MA0055.1	0.0983
MA0057.1	MA0057.1	0.0628
MA0058.1	MA0058.1	0.648
MA0059.1	MA0059.1	0.445
MA0060.1	MA0060.1	0.312
MA0061.1	MA0061.1	0.0121
MA0062.2	MA0062.2	7.38546e-8
MA0065.2	MA0065.2	4.39535e-10
MA0066.1	MA0066.1	0.0786
MA0067.1	MA0067.1	0.649
MA0068.1	MA0068.1	0.19
MA0069.1	MA0069.1	0.761
MA0070.1	MA0070.1	0.0621
MA0071.1	MA0071.1	0.211
MA0072.1	MA0072.1	0.979
MA0073.1	MA0073.1	0.761
MA0074.1	MA0074.1	0.394
MA0076.1	MA0076.1	0.0063
MA0077.1	MA0077.1	0.88
MA0078.1	MA0078.1	0.734
MA0079.2	MA0079.2	0.629
MA0080.2	MA0080.2	1.6297e-8
MA0081.1	MA0081.1	0.283
MA0083.1	MA0083.1	0.00551
MA0084.1	MA0084.1	0.457
MA0087.1	MA0087.1	0.329
MA0088.1	MA0088.1	0.0978
MA0090.1	MA0090.1	0.93
MA0091.1	MA0091.1	0.865
MA0092.1	MA0092.1	0.734
MA0093.1	MA0093.1	0.682
MA0099.2	MA0099.2	5.91584e-10
MA0100.1	MA0100.1	0.778
MA0101.1	MA0101.1	3.93515e-4
MA0102.2	MA0102.2	0.625
MA0103.1	MA0103.1	2.23412e-7
MA0104.2	MA0104.2	0.793
MA0105.1	MA0105.1	0.0353
MA0106.1	MA0106.1	0.218
MA0107.1	MA0107.1	8.76946e-4
MA0108.2	MA0108.2	0.1
MA0111.1	MA0111.1	0.737
MA0112.2	MA0112.2	9.89002e-4
MA0113.1	MA0113.1	0.245
MA0114.1	MA0114.1	7.79195e-18
MA0115.1	MA0115.1	1.05904e-11
MA0116.1	MA0116.1	0.0563
MA0117.1	MA0117.1	0.469
MA0119.1	MA0119.1	0.243
MA0122.1	MA0122.1	0.989
MA0124.1	MA0124.1	0.175
MA0125.1	MA0125.1	0.484
MA0131.1	MA0131.1	0.967
MA0135.1	MA0135.1	0.834
MA0136.1	MA0136.1	5.5859e-17
MA0137.2	MA0137.2	2.21405e-4
MA0138.2	MA0138.2	0.592
MA0139.1	MA0139.1	0.0804
MA0140.1	MA0140.1	0.259
MA0141.1	MA0141.1	4.36769e-5
MA0142.1	MA0142.1	0.172
MA0143.1	MA0143.1	0.0931
MA0144.1	MA0144.1	5.02537e-4
MA0145.1	MA0145.1	0.0173
MA0146.1	MA0146.1	0.143
MA0147.1	MA0147.1	0.905
MA0148.1	MA0148.1	0.0257
MA0149.1	MA0149.1	0.00644
MA0150.1	MA0150.1	0.0095
MA0152.1	MA0152.1	0.106
MA0153.1	MA0153.1	6.55911e-35
MA0154.1	MA0154.1	0.0582
MA0155.1	MA0155.1	0.761
MA0156.1	MA0156.1	1.36516e-9
MA0157.1	MA0157.1	0.35
MA0159.1	MA0159.1	5.07153e-4
MA0160.1	MA0160.1	0.00211
MA0162.1	MA0162.1	0.354
MA0163.1	MA0163.1	0.0531
MA0164.1	MA0164.1	0.575
MA0258.1	MA0258.1	0.0414
MA0259.1	MA0259.1	0.837

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: CNhs13234

Novel motif	Logo	P-value
1	1	0.0983
10	10	0.0873
100	100	0.719
101	101	0.976
102	102	0.94
103	103	0.296
104	104	0.98
105	105	0.282
106	106	0.03
107	107	0.277
108	108	0.899
109	109	0.0148
11	11	0.0958
110	110	0.178
111	111	0.162
112	112	0.0199
113	113	0.328
114	114	0.23
115	115	0.875
116	116	0.131
117	117	0.0164
118	118	0.683
119	119	0.121
12	12	0.624
120	120	0.407
121	121	0.426
122	122	0.827
123	123	0.0671
124	124	0.248
125	125	0.408
126	126	0.046
127	127	0.116
128	128	0.224
129	129	0.12
13	13	1.51766e-4
130	130	0.84
131	131	0.743
132	132	0.636
133	133	0.882
134	134	0.95
135	135	0.223
136	136	0.0141
137	137	0.884
138	138	0.233
139	139	0.0907
14	14	0.702
140	140	0.241
141	141	0.109
142	142	0.828
143	143	0.698
144	144	0.126
145	145	0.0878
146	146	0.242
147	147	0.773
148	148	0.482
149	149	0.688
15	15	0.117
150	150	0.438
151	151	0.842
152	152	0.0491
153	153	0.865
154	154	0.918
155	155	0.25
156	156	0.114
157	157	0.491
158	158	0.629
159	159	0.658
160	160	0.822
161	161	0.55
162	162	0.71
163	163	0.233
164	164	0.0661
165	165	0.0375
166	166	0.371
167	167	0.563
168	168	0.824
169	169	0.0195
17	17	0.0296
18	18	0.897
19	19	0.308
2	2	0.933
20	20	0.297
21	21	0.945
22	22	0.333
23	23	0.913
24	24	0.31
25	25	0.475
26	26	0.00604
27	27	0.887
28	28	0.341
29	29	0.0494
3	3	0.116
30	30	0.576
31	31	0.933
32	32	0.214
33	33	0.164
34	34	0.848
35	35	0.754
36	36	0.19
37	37	0.0426
38	38	0.383
39	39	0.284
4	4	0.329
40	40	0.101
41	41	0.212
42	42	0.616
43	43	0.296
44	44	0.127
45	45	0.494
46	46	0.236
47	47	0.238
48	48	0.12
49	49	0.309
5	5	0.59
50	50	0.371
51	51	0.732
52	52	0.211
53	53	0.527
54	54	0.606
55	55	0.653
56	56	0.434
57	57	0.892
58	58	0.312
59	59	0.187
6	6	0.399
60	60	0.0548
61	61	0.171
62	62	0.222
63	63	0.0997
64	64	0.567
65	65	0.255
66	66	0.908
67	67	0.595
68	68	0.112
69	69	0.939
7	7	0.0874
70	70	0.00497
71	71	0.0766
72	72	0.211
73	73	0.0294
74	74	0.879
75	75	0.0181
76	76	0.633
77	77	0.105
78	78	0.0332
79	79	0.983
8	8	0.132
80	80	0.873
81	81	0.922
82	82	0.161
83	83	0.045
84	84	0.522
85	85	0.106
86	86	0.193
87	87	0.00873
88	88	0.258
89	89	0.122
9	9	0.927
90	90	0.0775
91	91	0.916
92	92	0.573
93	93	0.297
94	94	0.697
95	95	0.00416
96	96	0.621
97	97	0.977
98	98	0.458
99	99	0.198

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: CNhs13234

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011478 mouse Ileum epithelium 3days after RANKL 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0002108 (small intestine)
0000160 (intestine)
0000331 (ileal mucosa)
0000483 (epithelium)
0002116 (ileum)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0001204 (mucosa of small intestine)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001168 (wall of small intestine)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011478 (mouse Ileum epithelium 3days after RANKL 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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0002108,UBERON:0000160,UBERON:0000331,UBERON:0000483,UBERON:0002116,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0000062,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004923,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0001204,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0001262,UBERON:0004786,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0007026,UBERON:0001168,UBERON:0006595
+|DRA_sample_Accession=CAGE@SAMD00005036
+|accession_numbers=CAGE;DRX008919;DRR009793;DRZ001218;DRZ002601;DRZ012568;DRZ013951
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0002108,UBERON:0000160,UBERON:0000331,UBERON:0000483,UBERON:0002116,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0001204,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0001262,UBERON:0004786,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001168
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000998,FF:0000004,FF:0000383,FF:0000627,FF:0011478
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr7:51787434..51787448,-!p1@Spib!2.54!491.35!Spib;;chr10:80555320..80555378,-!p1@Creb3l3!2.25!203.33!Creb3l3;;chr5:148118639..148118715,-!p1@Cdx2!2.15!139.03!Cdx2;;chr3:3634145..3634161,+!p1@Hnf4g!2.03!106.87!Hnf4g;;chr10:88969376..88969395,-!p1@Nr1h4!1.97!93.13!Nr1h4;;chr17:27865882..27865901,-!p1@Spdef!1.93!84.04!Spdef;;chr2:163332558..163332596,+!p2@Hnf4a!1.93!83.37!Hnf4a;;chr18:61195865..61195880,-!p1@Cdx1!1.92!81.38!Cdx1;;chr1:137155026..137155042,-!p1@Elf3!1.89!423.28!Elf3;;chr2:163372884..163372904,+!p1@Hnf4a!1.86!70.73!Hnf4a;;chr6:64679112..64679126,+!p1@Atoh1!1.82!64.52!Atoh1;;chr6:86619104..86619119,-!p1@Mxd1!1.80!481.60!Mxd1;;chr18:61195843..61195864,-!p2@Cdx1!1.72!51.22!Cdx1;;chr16:38294860..38294924,-!p1@Nr1i2!1.64!42.57!Nr1i2;;chr2:180069370..180069409,-!p1@Gata5!1.63!48.56!Gata5;;chr8:77396591..77396639,+!p1@Isx!1.47!28.82!Isx;;chr2:103123925..103123959,-!p3@Ehf!1.44!26.61!Ehf;;chr4:124805061..124805087,-!p1@Zc3h12a!1.42!75.83!Zc3h12a;;chr7:19608891..19608895,-!p1@Foxa3!1.42!32.37!Foxa3;;chr3:3508024..3508069,+!p2@Hnf4g!1.40!24.17!Hnf4g;;chr2:103143336..103143367,-!p1@Ehf!1.33!32.59!Ehf;;chr5:148118840..148118857,-!p2@Cdx2!1.33!20.18!Cdx2;;chr12:58646974..58647003,-!p1@Foxa1!1.28!24.17!Foxa1;;chr5:148118792..148118806,-!p3@Cdx2!1.27!17.52!Cdx2;;chr2:173044357..173044377,-!p2@Zbp1!1.25!24.17!Zbp1;;chr2:173044380..173044432,-!p1@Zbp1!1.24!38.36!Zbp1;;chr5:120121169..120121171,+!p4@Tbx3!1.24!29.49!Tbx3;;chr14:99697871..99697934,+!p1@Klf5!1.20!290.47!Klf5;;chr3:90046995..90047031,-!p2@Creb3l4!1.20!18.40!Creb3l4;;chr4:122673187..122673201,+!p2@Mycl1!1.17!24.61!Mycl1;;chr10:61595830..61595846,+!p1@Neurog3!1.17!13.75!Neurog3;;chr4:87452180..87452196,-!p3@Mllt3!1.16!26.16!Mllt3;;chr6:39068163..39068176,-!p2@Parp12!1.16!25.28!Parp12;;chr5:115421065..115421088,-!p1@Hnf1a!1.16!13.53!Hnf1a;;chr4:133109285..133109308,+!p1@Nr0b2!1.15!13.08!Nr0b2;;chr2:133377954..133377973,+!p1@Bmp2!1.11!38.58!Bmp2;;chr17:25707623..25707639,-!p1@Sox8!1.09!49.00!Sox8;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.08!14.19!Zbtb11;;chr8:77397492..77397514,+!p3@Isx!1.07!10.64!Isx;;chr1:194979315..194979359,+!p1@Irf6!1.06!64.75!Irf6;;chr15:35225845..35225867,+!p1@Osr2!1.06!26.61!Osr2;;chr7:20213752..20213778,-!p2@Relb!1.06!10.42!Relb;;chr5:148118614..148118625,-!p4@Cdx2!1.06!10.42!Cdx2;;chr19:5560600..5560617,-!p1@Ovol1!1.04!12.20!Ovol1;;chr15:97738692..97738747,-!p1@Vdr!1.03!53.66!Vdr;;chr19:46380235..46380277,+!p3@Nfkb2!1.02!20.84!Nfkb2;;chr5:148118809..148118832,-!p5@Cdx2!1.02!9.53!Cdx2;;chr7:20214704..20214800,-!p1@Relb!1.00!30.38!Relb;;chr2:103143315..103143328,-!p2@Ehf!1.00!9.09!Ehf;;chr5:135582751..135582788,+!p1@Mlxipl!0.99!35.92!Mlxipl;;chr10:20880629..20880683,-!p1@Myb!0.99!25.72!Myb;;chr8:77397190..77397202,+!p5@Isx!0.99!8.87!Isx;;chr3:128918394..128918413,+!p5@Pitx2!0.98!8.65!Pitx2;;chr8:77397095..77397127,+!p2@Isx!0.97!8.43!Isx;;chr10:80555398..80555409,-!p2@Creb3l3!0.96!8.20!Creb3l3;;chr7:150155143..150155156,-!p1@Ascl2!0.96!8.20!Ascl2;;chr11:53583544..53583559,+!p1@Irf1!0.95!137.92!Irf1;;chr19:6996243..6996293,-!p1@Esrra!0.95!90.69!Esrra;;chr7:148452314..148452329,-!p1@Irf7!0.95!56.54!Irf7;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.95!23.28!Tfcp2l1;;chr8:87643578..87643593,-!p1@Zfp791!0.95!16.85!Zfp791;;chr11:96153767..96153822,+!p1@Hoxb6!0.95!12.42!Hoxb6;;chr11:70500401..70500460,-!p3@Camta2!0.95!7.98!Camta2;;chr2:152561980..152561997,+!p1@Id1!0.93!223.95!Id1;;chr19:46379199..46379301,+!p1@Nfkb2!0.92!43.24!Nfkb2;;chr2:28477452..28477483,-!p1@Gfi1b!0.92!9.09!Gfi1b;;chr8:77396650..77396662,+!p4@Isx!0.92!7.32!Isx;;chr12:56593574..56593592,-!p1@Nfkbia!0.90!370.07!Nfkbia;;chr2:163372869..163372882,+!p3@Hnf4a!0.90!6.87!Hnf4a;;chr14:63864056..63864102,-!p1@Gata4!0.89!11.97!Gata4;;chr2:79296783..79296801,-!p1@Neurod1!0.88!6.65!Neurod1;;chr17:34784073..34784118,+!p2@Atf6b!0.87!27.05!Atf6b;;chr3:89197057..89197114,-!p1@Zbtb7b!0.87!22.62!Zbtb7b;;chr5:144951153..144951203,+!p1@Bhlha15!0.86!9.31!Bhlha15;;chr17:28409136..28409150,+!p3@Ppard!0.86!6.21!Ppard;;chr11:100948597..100948637,+!p1@Mlx!0.84!150.78!Mlx;;chr4:87452200..87452229,-!p2@Mllt3!0.84!13.08!Mllt3;;chr10:88996336..88996380,-!p2@Nr1h4!0.84!7.54!Nr1h4;;chr2:147871627..147871641,-!p1@Foxa2!0.83!5.76!Foxa2;;chr7:20408047..20408125,-!p1@Bcl3!0.82!68.96!Bcl3;;chr8:125778192..125778217,+!p2@Zfp276!0.82!16.63!Zfp276;;chr8:123260252..123260264,+!p1@Irf8!0.81!41.02!Irf8;;chr18:11052606..11052633,+!p4@Gata6!0.80!14.19!Gata6;;chr9:31720843..31720888,-!p1@Barx2!0.80!5.99!Barx2;;chr3:3508005..3508021,+!p3@Hnf4g!0.79!5.10!Hnf4g;;chr12:86814833..86814846,+!p1@Fos!0.78!129.05!Fos;;chr18:11052642..11052659,+!p1@Gata6!0.77!26.61!Gata6;;chr7:20162663..20162678,+!p1@Zfp296!0.77!6.65!Zfp296;;chr14:76887526..76887555,+!p10@Tsc22d1!0.77!4.88!Tsc22d1;;chr4:43575544..43575565,+!p2@Creb3!0.76!30.60!Creb3;;chr3:135354384..135354443,-!p1@Nfkb1!0.75!31.26!Nfkb1;;chr19:55816546..55816556,+!p3@Tcf7l2!0.75!19.29!Tcf7l2;;chr7:134519473..134519502,-!p3@Zfp747!0.75!6.43!Zfp747;;chr5:77524250..77524300,-!p1@Hopx!0.74!101.77!Hopx;;chr1:39250584..39250643,+!p1@Npas2!0.73!24.17!Npas2;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.73!21.73!Hmga1;;chr17:45692642..45692663,+!p1@Nfkbie!0.72!15.08!Nfkbie;;chr8:73905344..73905381,-!p2@Nr2f6!0.72!11.09!Nr2f6;;chr4:148178559..148178603,+!p1@Casz1!0.71!13.08!Casz1;;chr12:78063146..78063159,-!p2@Max!0.71!11.75!Max;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.71!11.09!Hmga1;;chr8:87502608..87502623,-!p1@Junb!0.70!74.06!Junb;;chr5:77524231..77524245,-!p3@Hopx!0.70!10.86!Hopx;;chr10:127095407..127095440,+!p3@Stat6!0.70!5.10!Stat6;;chr10:88996295..88996335,-!p3@Nr1h4!0.70!4.88!Nr1h4;;chr10:80555299..80555306,-!p3@Creb3l3!0.70!3.99!Creb3l3;;chr3:128918433..128918448,+!p8@Pitx2!0.70!3.99!Pitx2;;chr13:44825008..44825066,+!p5@Jarid2!0.69!8.20!Jarid2;;chr10:80555285..80555291,-!p4@Creb3l3!0.68!3.77!Creb3l3;;chr9:31720903..31720918,-!p2@Barx2!0.68!3.77!Barx2;;chr8:77397026..77397036,+!p6@Isx!0.68!3.77!Isx;;chr3:90046983..90046994,-!p6@Creb3l4!0.68!3.77!Creb3l4;;chr2:146047829..146047847,+!p1@Insm1!0.67!7.10!Insm1;;chr8:118231678..118231692,-!p2@Maf!0.66!37.69!Maf;;chr4:124805092..124805135,-!p2@Zc3h12a!0.66!17.07!Zc3h12a;;chr7:29551488..29551529,-!p1@Nfkbib!0.65!130.38!Nfkbib;;chr7:29551464..29551487,-!p2@Nfkbib!0.64!15.08!Nfkbib;;chr12:78063032..78063043,-!p4@Max!0.64!4.88!Max;;chr19:5560570..5560582,-!p2@Ovol1!0.64!3.33!Ovol1;;chr6:39068210..39068251,-!p1@Parp12!0.62!17.07!Parp12;;chr15:79177964..79177986,+!p1@Maff!0.62!12.42!Maff;;chr4:135700687..135700719,+!p2@Id3!0.62!5.32!Id3;;chr19:6164433..6164446,+!p2@Batf2!0.61!3.10!Batf2;;chr2:180069640..180069660,-!p4@Gata5!0.61!3.10!Gata5;;chr11:98636400..98636418,-!p4@Nr1d1!0.60!4.21!Nr1d1;;chr6:39068181..39068206,-!p3@Parp12!0.59!6.65!Parp12;;chr11:96145450..96145517,+!p2@Hoxb7!0.59!4.66!Hoxb7;;chr7:31206743..31206761,+!p1@Nfkbid!0.59!4.21!Nfkbid;;chr1:138857048..138857071,-!p2@Nr5a2!0.59!2.88!Nr5a2;;chr10:107769168..107769215,+!p1@Pawr!0.58!35.26!Pawr;;chr1:194979361..194979373,+!p2@Irf6!0.58!3.99!Irf6;;chr19:6996294..6996324,-!p2@Esrra!0.57!21.95!Esrra;;chr16:87699206..87699229,+!p3@Bach1!0.57!17.96!Bach1;;chr13:5860776..5860796,+!p1@Klf6!0.56!79.38!Klf6;;chr8:118231705..118231722,-!p3@Maf!0.56!25.72!Maf;;chr10:80600749..80600766,+!p2@Zbtb7a!0.56!16.85!Zbtb7a;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.56!5.99!Hmga1;;chr7:134519511..134519534,-!p2@Zfp747!0.56!5.54!Zfp747;;chr13:55932591..55932622,-!p1@Pitx1!0.56!3.33!Pitx1;;chr1:173144100..173144138,+!p2@Nr1i3!0.56!2.66!Nr1i3;;chr3:89197216..89197258,-!p3@Zbtb7b!0.55!6.21!Zbtb7b;;chr17:45692676..45692695,+!p2@Nfkbie!0.55!5.99!Nfkbie;;chr16:55822241..55822258,-!p1@Nfkbiz!0.54!97.12!Nfkbiz;;chr7:87170879..87170914,+!p2@Zfp710!0.54!6.65!Zfp710;;chr13:112476433..112476448,+!p2@Mier3!0.54!5.32!Mier3;;chr13:55932624..55932641,-!p2@Pitx1!0.54!2.44!Pitx1;;chr10:20880698..20880717,-!p3@Myb!0.53!4.21!Myb;;chr11:106128936..106128955,-!p4@Smarcd2!0.53!2.88!Smarcd2;;chr14:79915425..79915501,+!p1@Elf1!0.52!26.61!Elf1;;chr19:46380172..46380231,+!p2@Nfkb2!0.52!19.96!Nfkb2;;chr10:80598209..80598236,+!p4@Zbtb7a!0.52!4.43!Zbtb7a;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.52!3.55!Carhsp1;;chr1:138846009..138846038,-!p3@Nr5a2!0.52!2.66!Nr5a2;;chr2:166888058..166888105,-!p2@Znfx1!0.51!8.87!Znfx1;;chr15:37162796..37162828,+!p1@Grhl2!0.51!4.21!Grhl2;;chr13:55932739..55932756,-!p5@Pitx1!0.51!2.22!Pitx1;;chr1:138857076..138857105,-!p1@Nr5a2!0.51!2.22!Nr5a2;;chr1:138846079..138846103,-!p6@Nr5a2!0.51!2.22!Nr5a2;;chr4:148178459..148178482,+!p4@Casz1!0.51!2.22!Casz1;;chr11:98822047..98822072,+!p9@Rara!0.51!2.22!Rara;;chr8:77397169..77397182,+!p7@Isx!0.51!2.22!Isx;;chr9:43013917..43013968,-!p1@Pou2f3!0.51!2.22!Pou2f3;;chr11:96690797..96690813,-!p1@Nfe2l1!0.50!55.43!Nfe2l1;;chr4:55545337..55545357,-!p1@Klf4!0.50!42.57!Klf4;;chr4:135728581..135728668,+!p1@E2f2!0.50!13.30!E2f2;;chr18:11052485..11052508,+!p2@Gata6!0.50!7.54!Gata6;;chr10:30375579..30375616,-!p3@Ncoa7!0.50!6.21!Ncoa7;;chr4:135699731..135699747,+!p1@Id3!0.49!317.52!Id3;;chr4:122673278..122673336,+!p1@Mycl1!0.48!7.98!Mycl1;;chrX:103123886..103123922,-!p3@Atrx!0.48!6.65!Atrx;;chr5:32438894..32438908,+!p2@Fosl2!0.48!5.10!Fosl2;;chr10:80599248..80599261,+!p3@Zbtb7a!0.48!4.21!Zbtb7a;;chr2:28477422..28477433,-!p2@Gfi1b!0.48!2.00!Gfi1b;;chr15:35225873..35225889,+!p2@Osr2!0.48!2.00!Osr2;;chr5:115420882..115420896,-!p3@Hnf1a!0.48!2.00!Hnf1a;;chr15:81977802..81977828,+!p2@Srebf2!0.47!22.17!Srebf2;;chr17:21625946..21626024,+!p1@Zfp53!0.46!28.16!Zfp53;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.46!14.86!Zbtb11;;chr8:79426176..79426275,+!p1@Nr3c2!0.46!12.64!Nr3c2;;chr6:52664406..52664434,+!p3@Tax1bp1!0.46!2.44!Tax1bp1;;chr13:5860872..5860883,+!p3@Klf6!0.45!4.43!Klf6;;chr5:104182694..104182724,+!p8@Aff1!0.45!2.44!Aff1;;chr11:98636373..98636387,-!p5@Nr1d1!0.45!2.22!Nr1d1;;chr12:86940338..86940357,+!p1@Jdp2!0.44!23.95!Jdp2;;chr5:120121020..120121049,+!p1@Tbx3!0.44!14.63!Tbx3;;chrX:7339938..7339963,+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2;;chr6:16848395..16848416,-!p2@Tfec!0.03!0.22!Tfec;;chr12:75008961..75009002,+!p1@Hif1a!0.02!56.54!Hif1a;;chr1:172797892..172797915,-!p1@Atf6!0.02!25.94!Atf6;;chr7:147222284..147222351,+!p1@Zfp511!0.02!21.06!Zfp511;;chr7:52253030..52253070,+!p1@Irf3!0.02!20.18!Irf3;;chr19:41557122..41557178,+!p1@Lcor!0.02!18.85!Lcor;;chr12:85658052..85658097,+!p1@Zfp410!0.02!15.52!Zfp410;;chr5:138596922..138596968,-!p1@Zfp113!0.02!8.65!Zfp113;;chr8:107694661..107694713,+!p2@Cbfb!0.02!5.54!Cbfb;;chr4:129055091..129055168,-!p1@Zbtb8a!0.02!4.66!Zbtb8a;;chr4:6917606..6917681,-!p1@Tox!0.02!3.10!Tox;;chr10:13685585..13685645,+!p2@Hivep2!0.02!2.44!Hivep2;;chr3:87945895..87945946,+!p2@Mef2d!0.02!2.22!Mef2d;;chrX:98449805..98449834,+!p3@Foxo4!0.02!1.77!Foxo4;;chr19:5637489..5637500,+!p5@Rela!0.02!1.55!Rela;;chr2:31428187..31428198,+!p3@Fubp3!0.02!1.11!Fubp3;;chr9:19426687..19426708,+!p3@Zfp317!0.02!0.89!Zfp317;;chr7:56136974..56136989,-!p4@E2f8!0.02!0.67!E2f8;;chr10:5958477..5958503,+!p4@Zbtb2!0.02!0.67!Zbtb2;;chr11:102178005..102178022,-!p8@Ubtf!0.02!0.67!Ubtf;;chr10:82226709..82226720,-!p6@Nfyb!0.02!0.67!Nfyb;;chr5:125342568..125342602,+!p2@Zfp664!0.02!0.67!Zfp664;;chr15:100382267..100382287,-!p3@Tfcp2!0.02!0.67!Tfcp2;;chr2:153067138..153067147,-!p3@Plagl2!0.02!0.67!Plagl2;;chr1:87546583..87546595,+!p1@Sp100!0.02!0.44!Sp100;;chr2:154395552..154395561,-!p3@E2f1!0.02!0.44!E2f1;;chr8:118230847..118230856,-!p8@Maf!0.02!0.44!Maf;;chr4:102786990..102786999,+!p11@Mier1!0.02!0.44!Mier1;;chr4:102792039..102792052,+!p7@Mier1!0.02!0.44!Mier1;;chr13:64254572..64254585,-!p6@Zfp367!0.02!0.44!Zfp367;;chr13:37917863..37917872,+!p14@Rreb1!0.02!0.44!Rreb1;;chr17:46693053..46693064,-!p4@Srf!0.02!0.44!Srf;;chr7:25292118..25292129,+!p8@Zfp428!0.02!0.22!Zfp428;;chr8:73905967..73905978,-!p4@Nr2f6!0.02!0.22!Nr2f6;;chr1:179374784..179374800,+!p2@Zfp238!0.02!0.22!Zfp238;;chr2:56976467..56976482,-!p4@Nr4a2!0.02!0.22!Nr4a2;;chr11:100800621..100800633,-!p5@Stat3!0.02!0.22!Stat3;;chr11:100800901..100800921,-!p4@Stat3!0.02!0.22!Stat3;;chr11:98636568..98636574,-!p9@Nr1d1!0.02!0.22!Nr1d1;;chr14:56223387..56223401,+!p3@Irf9!0.02!0.22!Irf9;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.02!0.22!Ncoa4;;chr13:37918661..37918673,+!p17@Rreb1!0.02!0.22!Rreb1;;chr4:108132526..108132533,+!p11@Zcchc11!0.02!0.22!Zcchc11;;chr19:4397052..4397098,-!p1@Kdm2a!0.01!23.73!Kdm2a;;chr16:3744089..3744145,+!p1@Zfp263!0.01!18.63!Zfp263;;chr2:83484658..83484678,+!p2@Zc3h15!0.01!13.97!Zc3h15;;chr15:10400285..10400360,-!p1@Dnajc21!0.01!11.31!Dnajc21;;chr10:85379647..85379751,-!p1@Prdm4!0.01!9.53!Prdm4;;chr2:181022663..181022712,-!p1@Gmeb2!0.01!8.87!Gmeb2;;chr19:55816770..55816793,+!p2@Tcf7l2!0.01!7.32!Tcf7l2;;chr2:120996843..120996894,-!p1@Zscan29!0.01!4.88!Zscan29;;chr17:48061692..48061723,-!p5@Foxp4!0.01!3.55!Foxp4;;chr8:72662966..72662991,-!p3@LOC100048268,p3@Rfxank!0.01!2.44!Rfxank;;chr9:18278055..18278126,-!p1@Zfp558!0.01!1.77!Zfp558;;chr7:97591412..97591431,+!p2@Crebzf!0.01!1.55!Crebzf;;chr13:5860740..5860747,+!p4@Klf6!0.01!1.11!Klf6;;chr15:25914217..25914232,+!p3@Zfp622!0.01!0.89!Zfp622;;chr11:3189171..3189197,+!p4@Patz1!0.01!0.89!Patz1;;chr11:58717721..58717738,-!p2@Zfp39!0.01!0.89!Zfp39;;chr19:9016651..9016662,+!p3@Mta2!0.01!0.89!Mta2;;chr15:88582079..88582091,+!p1@Gm15583,p1@Zbed4!0.01!0.67!Zbed4;;chr15:96118197..96118200,+!p3@Arid2!0.01!0.67!Arid2;;chr11:120494908..120494919,-!p4@Mafg!0.01!0.44!Mafg;;chr5:110539135..110539159,+!p4@Zfp605!0.01!0.44!Zfp605;;chr15:100058302..100058309,+!p3@Gm1862,p5@Atf1!0.01!0.44!Atf1;;chr4:63071739..63071760,-!p5@Akna!0.01!0.44!Akna;;chr3:95032515..95032553,-!p5@Mllt11!0.01!0.22!Mllt11;;chr4:154335024..154335039,+!p1@Hes5!0.01!0.22!Hes5;;chr4:6917793..6917809,-!p5@Tox!0.01!0.22!Tox;;chr6:29490887..29490891,+!p5@Irf5!0.01!0.22!Irf5;;chr18:35020615..35020641,+!p2@Egr1!0.01!0.22!Egr1;;chr18:74375754..74375763,+!p4@Cxxc1!0.01!0.22!Cxxc1;;chr2:156666435..156666476,+!p4@Tgif2!0.01!0.22!Tgif2;;chr1:14746065..14746079,-!p1@Msc!0.01!0.22!Msc;;chr1:69732682..69732719,-!p4@Ikzf2!0.01!0.22!Ikzf2;;chr2:153067233..153067236,-!p4@Plagl2!0.01!0.22!Plagl2;;chr19:9016729..9016740,+!p6@Mta2!0.01!0.22!Mta2;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011478
 |is_obsolete=
+|library_id=CNhs13234
+|library_id_phase_based=2:CNhs13234
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10260
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10260
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm9.nobarcode.rdna.fa.gz
 |name=Ileum epithelium, treated with RANKL, day03, pool3
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13234,LSID1006,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0308201765569842,0,0,0,0,0,-0.372867986823442,0,0,0,0,-0.0843392403965415,0,0,0,0,0.079702530423481,0,-0.104917931099179,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.336958598630687,0,0,0,0.0869754197833955,-0.0260319738423593,-0.0188880982256729,-0.149904844710197,-0.124513908935186,-0.984211366477826,-0.182893218226956,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.116558105764087,0,-0.087208855559089,0,0,-0.0206851859699652,-0.16352324777079,-0.310650657339386,-0.158091042771083,-0.0279167335058713,0,-0.0182827506450193,-0.132301710080237,-0.0523058587159848,0,0,-0.0998952837957378,-0.078232661647913,-0.508939460957174,0.00814382494348803,0,0,0,0,0,0.0869754197833955,-0.160203064613433,-0.847056771997041,-0.0793683749612458,0,0,0,0,0
 |rna_box=104
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=0.6149
 |sample_age=
+|sample_category=tissues
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10260-104C8;search_select_hide=table117:10260-104C8
 }}

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FF:10260-104C8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 13:57, 3 June 2020

CNhs13234

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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