FF:37-13H4: Difference between revisions

Latest revision as of 19:13, 4 June 2020

Name:	cecum, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10467
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	cecum
dev stage	adult
sex	male
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005238

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10467		CAGE		DRX008940		DRR009814

Accession ID Mm9

Library id		BAM		CTSS
CNhs10467		DRZ001239		DRZ002622

Accession ID Mm10

Library id		BAM		CTSS
CNhs10467		DRZ012589		DRZ013972

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

CNhs10467

0	0
1	0
10	0
100	0
1000	0.157
1001	-0.0275
1002	-0.0941
1003	-0.123
1004	0
1005	0
1006	-0.0932
1007	-0.0402
1008	0.819
1009	-0.0572
101	-0.0955
1010	0
1011	-0.108
1012	0
1013	0.24
1014	-0.0874
1015	-0.329
1016	-0.594
1017	0
1018	0.457
1019	0
102	0
1020	0
1021	0
1022	0.457
1023	0
1024	0.0546
1025	0.856
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0754
1030	0
1031	-0.556
1032	0.595
1033	-0.0752
1034	0
1035	0
1036	-0.186
1037	0
1038	0.109
1039	0.109
104	1.014
1040	-0.216
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: CNhs10467

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00189
MA0003.1	MA0003.1	0.0467
MA0004.1	MA0004.1	0.732
MA0006.1	MA0006.1	0.216
MA0007.1	MA0007.1	0.346
MA0009.1	MA0009.1	0.0141
MA0014.1	MA0014.1	0.617
MA0017.1	MA0017.1	2.10455e-6
MA0018.2	MA0018.2	0.0806
MA0019.1	MA0019.1	0.957
MA0024.1	MA0024.1	0.0107
MA0025.1	MA0025.1	0.698
MA0027.1	MA0027.1	0.223
MA0028.1	MA0028.1	0.157
MA0029.1	MA0029.1	0.978
MA0030.1	MA0030.1	0.118
MA0031.1	MA0031.1	0.0388
MA0035.2	MA0035.2	0.0118
MA0038.1	MA0038.1	0.568
MA0039.2	MA0039.2	0.00212
MA0040.1	MA0040.1	0.00846
MA0041.1	MA0041.1	0.131
MA0042.1	MA0042.1	0.32
MA0043.1	MA0043.1	0.0362
MA0046.1	MA0046.1	7.66484e-29
MA0047.2	MA0047.2	5.66148e-8
MA0048.1	MA0048.1	0.474
MA0050.1	MA0050.1	0.329
MA0051.1	MA0051.1	0.376
MA0052.1	MA0052.1	0.0292
MA0055.1	MA0055.1	0.252
MA0057.1	MA0057.1	0.0311
MA0058.1	MA0058.1	0.582
MA0059.1	MA0059.1	0.712
MA0060.1	MA0060.1	0.00249
MA0061.1	MA0061.1	0.251
MA0062.2	MA0062.2	0.109
MA0065.2	MA0065.2	1.18728e-6
MA0066.1	MA0066.1	0.19
MA0067.1	MA0067.1	0.416
MA0068.1	MA0068.1	0.00374
MA0069.1	MA0069.1	0.539
MA0070.1	MA0070.1	0.389
MA0071.1	MA0071.1	0.346
MA0072.1	MA0072.1	0.342
MA0073.1	MA0073.1	0.745
MA0074.1	MA0074.1	0.245
MA0076.1	MA0076.1	0.105
MA0077.1	MA0077.1	0.921
MA0078.1	MA0078.1	0.615
MA0079.2	MA0079.2	0.254
MA0080.2	MA0080.2	7.61443e-5
MA0081.1	MA0081.1	0.297
MA0083.1	MA0083.1	0.504
MA0084.1	MA0084.1	0.247
MA0087.1	MA0087.1	0.557
MA0088.1	MA0088.1	0.694
MA0090.1	MA0090.1	0.175
MA0091.1	MA0091.1	0.707
MA0092.1	MA0092.1	0.409
MA0093.1	MA0093.1	0.693
MA0099.2	MA0099.2	1.09565e-6
MA0100.1	MA0100.1	0.562
MA0101.1	MA0101.1	0.966
MA0102.2	MA0102.2	0.451
MA0103.1	MA0103.1	3.44406e-5
MA0104.2	MA0104.2	0.487
MA0105.1	MA0105.1	0.0138
MA0106.1	MA0106.1	0.173
MA0107.1	MA0107.1	0.913
MA0108.2	MA0108.2	1.08918e-9
MA0111.1	MA0111.1	0.538
MA0112.2	MA0112.2	1.43007e-4
MA0113.1	MA0113.1	0.37
MA0114.1	MA0114.1	6.04186e-7
MA0115.1	MA0115.1	0.00174
MA0116.1	MA0116.1	0.0399
MA0117.1	MA0117.1	0.794
MA0119.1	MA0119.1	0.0395
MA0122.1	MA0122.1	0.962
MA0124.1	MA0124.1	0.0565
MA0125.1	MA0125.1	0.473
MA0131.1	MA0131.1	0.266
MA0135.1	MA0135.1	0.62
MA0136.1	MA0136.1	0.00127
MA0137.2	MA0137.2	0.986
MA0138.2	MA0138.2	0.0128
MA0139.1	MA0139.1	0.183
MA0140.1	MA0140.1	0.614
MA0141.1	MA0141.1	0.0305
MA0142.1	MA0142.1	0.75
MA0143.1	MA0143.1	0.223
MA0144.1	MA0144.1	0.228
MA0145.1	MA0145.1	0.00719
MA0146.1	MA0146.1	0.569
MA0147.1	MA0147.1	0.521
MA0148.1	MA0148.1	6.14666e-6
MA0149.1	MA0149.1	0.0285
MA0150.1	MA0150.1	0.112
MA0152.1	MA0152.1	0.0676
MA0153.1	MA0153.1	5.69894e-22
MA0154.1	MA0154.1	0.0149
MA0155.1	MA0155.1	0.627
MA0156.1	MA0156.1	0.156
MA0157.1	MA0157.1	0.0933
MA0159.1	MA0159.1	0.00231
MA0160.1	MA0160.1	0.121
MA0162.1	MA0162.1	0.245
MA0163.1	MA0163.1	0.0235
MA0164.1	MA0164.1	0.658
MA0258.1	MA0258.1	0.0241
MA0259.1	MA0259.1	0.278

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: CNhs10467

Novel motif	Logo	P-value
1	1	0.218
10	10	0.312
100	100	0.917
101	101	0.517
102	102	0.937
103	103	0.214
104	104	0.757
105	105	0.0699
106	106	0.0199
107	107	0.0361
108	108	0.736
109	109	0.0799
11	11	0.291
110	110	0.214
111	111	0.217
112	112	0.113
113	113	0.704
114	114	0.0604
115	115	0.679
116	116	0.428
117	117	0.793
118	118	0.602
119	119	0.0589
12	12	0.555
120	120	0.164
121	121	0.486
122	122	0.596
123	123	0.721
124	124	0.468
125	125	0.213
126	126	0.0607
127	127	0.083
128	128	0.0168
129	129	0.287
13	13	0.0392
130	130	0.898
131	131	0.00626
132	132	0.382
133	133	0.124
134	134	0.695
135	135	0.994
136	136	0.708
137	137	0.596
138	138	0.992
139	139	0.00992
14	14	0.575
140	140	0.567
141	141	0.264
142	142	0.394
143	143	0.266
144	144	0.269
145	145	0.172
146	146	0.141
147	147	0.541
148	148	0.626
149	149	0.211
15	15	0.0982
150	150	0.539
151	151	0.304
152	152	0.0754
153	153	0.859
154	154	0.963
155	155	0.176
156	156	0.597
157	157	0.972
158	158	0.349
159	159	0.634
160	160	0.265
161	161	0.221
162	162	0.996
163	163	0.279
164	164	0.478
165	165	0.347
166	166	0.657
167	167	0.721
168	168	0.68
169	169	0.00875
17	17	0.049
18	18	0.303
19	19	0.142
2	2	0.384
20	20	0.573
21	21	0.892
22	22	0.316
23	23	0.165
24	24	0.278
25	25	0.597
26	26	0.0963
27	27	0.427
28	28	0.57
29	29	0.303
3	3	0.323
30	30	0.462
31	31	0.555
32	32	0.0691
33	33	0.414
34	34	0.61
35	35	0.758
36	36	0.381
37	37	0.111
38	38	0.409
39	39	0.519
4	4	0.103
40	40	0.226
41	41	0.255
42	42	0.676
43	43	0.21
44	44	0.343
45	45	0.309
46	46	0.219
47	47	0.326
48	48	0.258
49	49	0.172
5	5	0.0923
50	50	0.683
51	51	0.661
52	52	0.0872
53	53	0.838
54	54	0.516
55	55	0.704
56	56	0.347
57	57	0.747
58	58	0.243
59	59	0.189
6	6	0.39
60	60	0.055
61	61	0.295
62	62	0.139
63	63	0.17
64	64	0.456
65	65	0.096
66	66	0.751
67	67	0.313
68	68	0.94
69	69	0.597
7	7	0.0995
70	70	0.0252
71	71	0.187
72	72	0.531
73	73	0.111
74	74	0.53
75	75	0.282
76	76	0.4
77	77	0.118
78	78	0.0961
79	79	0.641
8	8	0.162
80	80	0.482
81	81	0.448
82	82	0.0918
83	83	0.0915
84	84	0.0244
85	85	0.0466
86	86	0.457
87	87	0.372
88	88	0.803
89	89	0.0929
9	9	0.545
90	90	0.351
91	91	0.258
92	92	0.232
93	93	0.14
94	94	0.727
95	95	0.283
96	96	0.168
97	97	0.37
98	98	0.384
99	99	0.131

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: CNhs10467

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011324 mouse cecum - adult 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)
0001155 (colon)
0000160 (intestine)
0001153 (caecum)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009854 (digestive tract diverticulum)
0010317 (germ layer / neural crest derived structure)
0009856 (sac)
0001555 (digestive tract)
0000059 (large intestine)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011324 (mouse cecum - adult 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:0001045 (midgut)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0001155,UBERON:0000160,UBERON:0001153,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000062,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0009854,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0009856,UBERON:0002532,UBERON:0001555,UBERON:0000059,UBERON:0005409,UBERON:0007026,UBERON:0006595,UBERON:0001045
+|DRA_sample_Accession=CAGE@SAMD00005238
+|accession_numbers=CAGE;DRX008940;DRR009814;DRZ001239;DRZ002622;DRZ012589;DRZ013972
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001155,UBERON:0000160,UBERON:0001153,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009854,UBERON:0010317,UBERON:0009856,UBERON:0001555,UBERON:0000059,UBERON:0005409
 |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:0011324
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr5:148118639..148118715,-!p1@Cdx2!2.55!356.01!Cdx2;;chr1:137155026..137155042,-!p1@Elf3!2.26!984.15!Elf3;;chr6:64679112..64679126,+!p1@Atoh1!2.11!128.61!Atoh1;;chr2:163332558..163332596,+!p2@Hnf4a!2.05!109.97!Hnf4a;;chr8:77396591..77396639,+!p1@Isx!2.02!104.38!Isx;;chr15:97738692..97738747,-!p1@Vdr!1.92!424.97!Vdr;;chr10:88969376..88969395,-!p1@Nr1h4!1.90!78.28!Nr1h4;;chr6:86619104..86619119,-!p1@Mxd1!1.86!544.26!Mxd1;;chr17:27865882..27865901,-!p1@Spdef!1.83!67.10!Spdef;;chr18:61195843..61195864,-!p2@Cdx1!1.81!63.37!Cdx1;;chr16:38294860..38294924,-!p1@Nr1i2!1.78!59.65!Nr1i2;;chr18:61195865..61195880,-!p1@Cdx1!1.78!59.65!Cdx1;;chr2:103143336..103143367,-!p1@Ehf!1.75!87.60!Ehf;;chr11:96153767..96153822,+!p1@Hoxb6!1.75!83.88!Hoxb6;;chr3:128916868..128916890,+!p1@Pitx2!1.75!74.56!Pitx2;;chr7:19608891..19608895,-!p1@Foxa3!1.71!65.24!Foxa3;;chr1:57029281..57029326,-!p1@Satb2!1.66!68.96!Satb2;;chr14:99697871..99697934,+!p1@Klf5!1.62!760.48!Klf5;;chr2:103143315..103143328,-!p2@Ehf!1.60!39.14!Ehf;;chr8:79426176..79426275,+!p1@Nr3c2!1.52!154.71!Nr3c2;;chr10:30375579..30375616,-!p3@Ncoa7!1.52!74.56!Ncoa7;;chr12:58646974..58647003,-!p1@Foxa1!1.50!41.01!Foxa1;;chr19:5560600..5560617,-!p1@Ovol1!1.50!37.28!Ovol1;;chr3:3634145..3634161,+!p1@Hnf4g!1.49!29.82!Hnf4g;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.43!72.69!Tfcp2l1;;chr2:163372884..163372904,+!p1@Hnf4a!1.43!26.09!Hnf4a;;chr3:3508024..3508069,+!p2@Hnf4g!1.43!26.09!Hnf4g;;chr11:70500401..70500460,-!p3@Camta2!1.43!26.09!Camta2;;chr5:148118840..148118857,-!p2@Cdx2!1.43!26.09!Cdx2;;chr7:148452314..148452329,-!p1@Irf7!1.42!167.75!Irf7;;chr5:148118614..148118625,-!p4@Cdx2!1.40!24.23!Cdx2;;chr5:148118792..148118806,-!p3@Cdx2!1.40!24.23!Cdx2;;chr8:77397492..77397514,+!p3@Isx!1.37!22.37!Isx;;chr3:90046995..90047031,-!p2@Creb3l4!1.34!26.09!Creb3l4;;chr5:144951153..144951203,+!p1@Bhlha15!1.31!27.96!Bhlha15;;chr2:103123925..103123959,-!p3@Ehf!1.29!18.64!Ehf;;chr4:87452180..87452196,-!p3@Mllt3!1.28!35.41!Mllt3;;chr11:98636531..98636559,-!p1@Nr1d1!1.26!95.06!Nr1d1;;chr6:52190467..52190500,-!p1@Hoxa10!1.25!16.78!Hoxa10;;chr6:115311030..115311065,+!p4@Pparg!1.22!22.37!Pparg;;chr6:52163319..52163342,-!p1@Hoxa3!1.22!22.37!Hoxa3;;chr11:98636400..98636418,-!p4@Nr1d1!1.22!20.50!Nr1d1;;chr13:55932591..55932622,-!p1@Pitx1!1.22!18.64!Pitx1;;chr5:148118809..148118832,-!p5@Cdx2!1.20!14.91!Cdx2;;chr13:31650185..31650201,+!p1@Foxq1!1.16!46.60!Foxq1;;chr10:22539932..22539956,-!p1@Tcf21!1.16!35.41!Tcf21;;chr6:52176164..52176195,-!p1@Hoxa9!1.16!16.78!Hoxa9;;chr6:52168685..52168715,-!p9@Hoxa7!1.15!13.05!Hoxa7;;chr1:138857048..138857071,-!p2@Nr5a2!1.15!13.05!Nr5a2;;chr8:77397190..77397202,+!p5@Isx!1.15!13.05!Isx;;chr2:173044380..173044432,-!p1@Zbp1!1.13!29.82!Zbp1;;chr8:123608252..123608268,+!p1@Foxf1a!1.13!18.64!Foxf1a;;chr4:55545051..55545110,-!p2@Klf4!1.11!14.91!Klf4;;chr11:83664365..83664383,+!p1@Hnf1b!1.09!11.18!Hnf1b;;chr5:115421065..115421088,-!p1@Hnf1a!1.09!11.18!Hnf1a;;chr6:72580544..72580553,-!p12@Tcf7l1!1.09!11.18!Tcf7l1;;chr17:28409136..28409150,+!p3@Ppard!1.09!11.18!Ppard;;chr2:180069370..180069409,-!p1@Gata5!1.08!13.05!Gata5;;chr2:74549968..74549996,+!p1@Hoxd3!1.06!13.05!Hoxd3;;chr4:124805061..124805087,-!p1@Zc3h12a!1.05!31.69!Zc3h12a;;chr18:36441119..36441158,+!p2@Pura!1.03!24.23!Pura;;chr11:98636373..98636387,-!p5@Nr1d1!1.03!11.18!Nr1d1;;chr14:99698164..99698208,+!p2@Klf5!1.03!11.18!Klf5;;chr6:52664406..52664434,+!p3@Tax1bp1!1.01!11.18!Tax1bp1;;chr1:57029027..57029056,-!p7@Satb2!1.01!9.32!Satb2;;chr11:96055681..96055693,+!p2@Hoxb13!1.01!9.32!Hoxb13;;chr8:77397095..77397127,+!p2@Isx!1.01!9.32!Isx;;chr8:59799772..59799789,+!p1@Hand2!1.00!26.09!Hand2;;chr1:189821714..189821761,+!p1@Esrrg!1.00!16.78!Esrrg;;chr11:98636508..98636524,-!p3@Nr1d1!1.00!11.18!Nr1d1;;chr8:123260252..123260264,+!p1@Irf8!0.96!59.65!Irf8;;chr3:89197057..89197114,-!p1@Zbtb7b!0.96!27.96!Zbtb7b;;chr4:55545152..55545194,-!p3@Klf4!0.95!9.32!Klf4;;chr1:194979315..194979359,+!p1@Irf6!0.94!48.46!Irf6;;chr4:87452200..87452229,-!p2@Mllt3!0.94!16.78!Mllt3;;chr14:118636214..118636235,-!p1@Sox21!0.94!9.32!Sox21;;chr4:55545337..55545357,-!p1@Klf4!0.93!115.56!Klf4;;chr3:128918394..128918413,+!p5@Pitx2!0.93!7.46!Pitx2;;chr8:77397026..77397036,+!p6@Isx!0.93!7.46!Isx;;chr19:43686789..43686811,+!p1@Nkx2-3!0.93!7.46!Nkx2-3;;chr19:5560570..5560582,-!p2@Ovol1!0.93!7.46!Ovol1;;chr2:147871627..147871641,-!p1@Foxa2!0.93!7.46!Foxa2;;chr1:194979383..194979393,+!p3@Irf6!0.93!7.46!Irf6;;chr1:189821700..189821713,+!p4@Esrrg!0.93!7.46!Esrrg;;chr11:96055613..96055628,+!p1@Hoxb13!0.93!7.46!Hoxb13;;chr11:96145450..96145517,+!p2@Hoxb7!0.92!11.18!Hoxb7;;chr16:55822241..55822258,-!p1@Nfkbiz!0.91!231.13!Nfkbiz;;chr5:135582751..135582788,+!p1@Mlxipl!0.91!29.82!Mlxipl;;chr18:11052606..11052633,+!p4@Gata6!0.91!18.64!Gata6;;chr19:53384910..53384937,+!p3@Mxi1!0.90!20.50!Mxi1;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.89!35.41!C130039O16Rik;;chr13:112476433..112476448,+!p2@Mier3!0.89!13.05!Mier3;;chr1:194979361..194979373,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b2!0.46!1.86!Satb2;;chr1:57028606..57028625,-!p4@Satb2!0.46!1.86!Satb2;;chr2:133378740..133378753,+!p2@Bmp2!0.46!1.86!Bmp2;;chr2:147871948..147871977,-!p3@Foxa2!0.46!1.86!Foxa2;;chr1:64579184..64579194,+!p7@Creb1!0.46!1.86!Creb1;;chr1:169619683..169619694,+!p1@Lmx1a!0.46!1.86!Lmx1a;;chr1:138857112..138857130,-!p7@Nr5a2!0.46!1.86!Nr5a2;;chr8:77397169..77397182,+!p7@Isx!0.46!1.86!Isx;;chr9:111020746..111020768,+!p5@Lrrfip2!0.46!1.86!Lrrfip2;;chr8:26958093..26958148,-!p2@Ash2l!0.46!1.86!Ash2l;;chr9:43013917..43013968,-!p1@Pou2f3!0.46!1.86!Pou2f3;;chr8:87502350..87502362,-!p2@Junb!0.46!1.86!Junb;;chr7:20213752..20213778,-!p2@Relb!0.46!1.86!Relb;;chr8:94881686..94881700,+!p4@Irx5!0.46!1.86!Irx5;;chr9:31720903..31720918,-!p2@Barx2!0.46!1.86!Barx2;;chr16:25801993..25802014,+!p1@Trp63!0.46!1.86!Trp63;;chr16:43364258..43364270,+!p27@Zbtb20!0.46!1.86!Zbtb20;;chr15:85566241..85566253,+!p6@Ppara!0.46!1.86!Ppara;;chr19:46380374..46380397,+!p7@Nfkb2!0.46!1.86!Nfkb2;;chr19:5447886..5447905,+!p1@Fosl1!0.46!1.86!Fosl1;;chr14:63890545..63890560,-!p5@Gata4!0.46!1.86!Gata4;;chr12:39510090..39510114,+!p6@Etv1!0.46!1.86!Etv1;;chr12:30213247..30213333,+!p1@Myt1l!0.46!1.86!Myt1l;;chr14:17408022..17408043,-!p6@Rarb!0.46!1.86!Rarb;;chr13:55937432..55937460,-!p4@Pitx1!0.46!1.86!Pitx1;;chr15:37163041..37163061,+!p5@Grhl2!0.46!1.86!Grhl2;;chr3:32264565..32264613,-!p1@Zmat3!0.45!27.96!Zmat3;;chr5:104183219..104183236,+!p2@Aff1!0.45!16.78!Aff1;;chr14:19071466..19071550,-!p1@Nr1d2!0.45!16.78!Nr1d2;;chr1:181733737..181733755,-!p2@Ahctf1!0.45!7.46!Ahctf1;;chr6:14851440..14851497,+!p2@Foxp2!0.45!5.59!Foxp2;;chr16:92826249..92826325,-!p1@Runx1!0.45!5.59!Runx1;;chr6:86619130..86619158,-!p2@Mxd1!0.44!35.41!Mxd1;;chr13:5860749..5860772,+!p2@Klf6!0.44!24.23!Klf6;;chr8:4613182..4613207,+!p2@Zfp958!0.44!9.32!Zfp958;;chr11:120494669..120494688,-!p2@Mafg!0.44!5.59!Mafg;;chr15:35225845..35225867,+!p1@Osr2!0.44!5.59!Osr2;;chr17:71200529..71200556,-!p1@Tgif1!0.43!39.14!Tgif1;;chr15:76709732..76709764,+!p1@Zfp7!0.43!11.18!Zfp7;;chr8:72663049..72663061,-!p4@LOC100048268,p4@Rfxank!0.43!3.73!Rfxank;;chr6:108610766..108610781,+!p2@Bhlhe40!0.43!3.73!Bhlhe40;;chr2:34227273..34227292,-!p4@Pbx3!0.43!1.86!Pbx3;;chr8:94325446..94325459,-!p8@Irx3!0.43!1.86!Irx3;;chr4:135699731..135699747,+!p1@Id3!0.42!272.13!Id3;;chr10:80599279..80599353,+!p1@Zbtb7a!0.42!42.87!Zbtb7a;;chrX:137077716..137077734,-!p1@Tsc22d3!0.42!16.78!Tsc22d3;;chr17:84587167..84587239,-!p2@Zfp36l2!0.42!7.46!Zfp36l2;;chr11:95170871..95170900,-!p2@Myst2!0.42!5.59!Myst2;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.42!3.73!Zbtb38;;chr9:96620459..96620478,-!p9@Zbtb38!0.42!1.86!Zbtb38;;chr6:115310968..115310980,+!p8@Pparg!0.42!1.86!Pparg;;chr2:74550178..74550214,+!p5@Hoxd3!0.42!1.86!Hoxd3;;chr3:29912154..29912168,-!p11@Mecom!0.42!1.86!Mecom;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.41!70.83!Zfp706;;chr7:35841486..35841575,-!p1@Cebpg!0.41!59.65!Cebpg;;chr7:7124057..7124084,+!p1@Zfp418!0.41!7.46!Zfp418;;chr5:77543897..77543911,-!p2@Hopx!0.41!3.73!Hopx;;chr5:120120667..120120685,+!p3@Tbx3!0.41!3.73!Tbx3;;chr13:29045296..29045307,-!p8@Sox4!0.41!1.86!Sox4;;chr1:69732354..69732402,-!p1@Ikzf2!0.41!1.86!Ikzf2;;chr12:78063165..78063227,-!p1@Max!0.40!195.71!Max;;chr7:51809271..51809325,-!p1@Nr1h2!0.40!126.75!Nr1h2;;chr2:27532754..27532815,+!p1@Rxra!0.40!67.10!Rxra;;chr11:5420954..5420969,+!p2@Xbp1!0.40!27.96!Xbp1;;chr15:102076870..102076941,-!p1@Rarg!0.40!24.23!Rarg;;chr5:104121391..104121450,+!p3@Aff1!0.40!11.18!Aff1;;chr6:72849280..72849297,-!p6@Kcmf1!0.40!3.73!Kcmf1;;chr8:94881733..94881790,+!p1@Irx5!0.40!3.73!Irx5;;chr11:58717721..58717738,-!p2@Zfp39!0.40!3.73!Zfp39;;chr11:106128936..106128955,-!p4@Smarcd2!0.40!1.86!Smarcd2;;chr3:30993641..30993651,+!p7@Skil!0.40!1.86!Skil;;chr1:36364572..36364580,+!p2@Arid5a!0.40!1.86!Arid5a;;chr18:5334737..5334749,-!p5@Zfp438!0.40!1.86!Zfp438;;chr8:107793737..107793757,+!p2@Hsf4!0.40!1.86!Hsf4;;chr13:112476296..112476308,+!p4@Mier3!0.40!1.86!Mier3;;chr16:23988711..23988727,-!p1@Bcl6!0.39!26.09!Bcl6;;chr1:135320989..135321043,-!p1@Sox13!0.39!24.23!Sox13;;chr1:135557964..135557976,-!p2@Zc3h11a!0.39!18.64!Zc3h11a;;chr17:48061409..48061431,-!p4@Foxp4!0.39!11.18!Foxp4;;chr8:81552216..81552249,+!p3@Zfp827!0.39!5.59!Zfp827;;chr19:55816278..55816287,+!p10@Tcf7l2!0.39!3.73!Tcf7l2;;chr17:48025139..48025166,-!p8@Foxp4!0.39!1.86!Foxp4;;chr15:85566051..85566080,+!p4@Ppara!0.39!1.86!Ppara;;chr1:52065508..52065522,+!p2@Stat4!0.39!1.86!Stat4;;chr1:194979301..194979310,+!p4@Irf6!0.39!1.86!Irf6;;chr10:88996295..88996335,-!p3@Nr1h4!0.39!1.86!Nr1h4;;chr12:109241852..109241873,-!p4@Bcl11b!0.39!1.86!Bcl11b;;chr10:67599450..67599456,-!p8@Arid5b!0.39!1.86!Arid5b;;chr10:67599461..67599470,-!p6@Arid5b!0.39!1.86!Arid5b;;chr14:22808697..22808715,-!p4@Zfp503!0.39!1.86!Zfp503;;chr5:137042233..137042245,-!p4@Cux1!0.39!1.86!Cux1;;chr5:104183173..104183207,+!p1@Aff1!0.38!27.96!Aff1;;chr6:39068210..39068251,-!p1@Parp12!0.38!9.32!Parp12;;chr17:45570455..45570479,-!p2@Cdc5l!0.38!7.46!Cdc5l;;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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0001045,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:37-13H4
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011324
+|is_a=EFO:0002091;;FF:0011324
+|is_obsolete=
+|library_id=CNhs10467
+|library_id_phase_based=2:CNhs10467
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;37
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;37
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cecum%252c%2520adult.CNhs10467.37-13H4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cecum%252c%2520adult.CNhs10467.37-13H4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cecum%252c%2520adult.CNhs10467.37-13H4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cecum%252c%2520adult.CNhs10467.37-13H4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cecum%252c%2520adult.CNhs10467.37-13H4.mm9.nobarcode.rdna.fa.gz
 |name=cecum, adult
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10467,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.110684663778904,0,0,0,0,0,-0.450392940864481,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.558422792324031,0,0,0,0,-0.000372900846334457,0.0191575346234575,-0.199560385736905,-0.255082692546983,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,0.097783694668497,0,0,0,-0.243225778194271,0.364011674663008,-0.158091042771083,-0.0365927089968535,0,-0.0780086007519514,-0.0973736644748266,0,0,0,-0.0528907212534099,0.084601241318938,0.223086034007709,-0.0788315948399074,0,0,0,0,0,0,0.101209360686936,0.201419247250039,-0.0413227421121155,0,0,0,0,0
 |rna_box=13
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=cecum
 |top_motifs=SNAI1..3:2.46112033319;ZEB1:2.44602078134;T:2.13292955426;FOSL2:1.79216296041;TBP:1.68283316226;ESRRA:1.62650976433;FOX{F1,F2,J1}:1.58951634714;NR1H4:1.54081330767;MYOD1:1.45546968064;TBX4,5:1.43473098029;FOXN1:1.4199309342;ATF6:1.37550768671;POU1F1:1.35225801448;NFE2L2:1.34606952956;FOXQ1:1.31374450359;JUN:1.29449055763;HNF4A_NR2F1,2:1.21473360802;FOS_FOS{B,L1}_JUN{B,D}:1.16705647396;ZNF148:1.10466305877;PPARG:1.09625967393;HNF1A:1.05341340644;NFIX:1.04565659629;HMX1:1.00555943781;AR:0.994291811897;PBX1:0.988730207373;SRF:0.954461020105;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.949125302505;EBF1:0.867161018141;AIRE:0.864709233579;FOX{D1,D2}:0.857629172899;BACH2:0.857508769184;POU2F1..3:0.821495690644;PDX1:0.804123252372;CDX1,2,4:0.763266467818;FOXM1:0.739315874066;FOXA2:0.685559172635;CDC5L:0.682808687182;RXRA_VDR{dimer}:0.67496429829;TLX1..3_NFIC{dimer}:0.618468467917;NR5A1,2:0.618269404159;ETS1,2:0.615384895046;TLX2:0.603888393423;bHLH_family:0.522974047713;HAND1,2:0.496613278949;POU6F1:0.489460225707;IRF1,2:0.486789971253;FOXO1,3,4:0.460575156901;NFE2:0.403439693917;ADNP_IRX_SIX_ZHX:0.379201569895;GATA6:0.37171132815;IRF7:0.35267348322;LMO2:0.348736365379;NKX3-2:0.319689076873;DMAP1_NCOR{1,2}_SMARC:0.2928382786;TFAP4:0.260337442303;NFKB1_REL_RELA:0.213148452691;NANOG:0.183234436961;MAFB:0.181126638188;STAT2,4,6:0.148622263857;TP53:0.0942725203285;SP1:0.0682256148336;XCPE1{core}:0.0537787662393;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0492362078158;EP300:0.0489865564218;NFE2L1:0.0411775413235;ARID5B:0.0409914796389;TFCP2:0.025829976265;GTF2A1,2:0.0231248077512;NKX3-1:-0.00344691464881;SPZ1:-0.00800569820423;NKX2-3_NKX2-5:-0.0568683217602;NR6A1:-0.0772485727762;FOX{I1,J2}:-0.101746412376;NR3C1:-0.109789017424;HLF:-0.116542698251;GFI1B:-0.128311963251;CEBPA,B_DDIT3:-0.134016954676;TEAD1:-0.141379455572;POU5F1:-0.142003352755;SMAD1..7,9:-0.177426418375;OCT4_SOX2{dimer}:-0.18279614243;RUNX1..3:-0.184072274314;GCM1,2:-0.201587348536;ZNF238:-0.203685045275;RBPJ:-0.210468992662;DBP:-0.218005465669;REST:-0.218317797397;YY1:-0.219808082162;ESR1:-0.227772252642;MYFfamily:-0.2508896357;PAX5:-0.264745958098;NFIL3:-0.265810786053;GTF2I:-0.278970037506;TOPORS:-0.285635522616;HOX{A5,B5}:-0.294234586359;HOXA9_MEIS1:-0.326766668857;CRX:-0.330699749324;SPI1:-0.344937240468;SREBF1,2:-0.361802138631;NKX6-1,2:-0.364400590685;ALX4:-0.374080517677;PRRX1,2:-0.379673518331;GFI1:-0.407297276974;LHX3,4:-0.411462259437;PAX8:-0.415873260298;ZBTB6:-0.418981898768;ATF5_CREB3:-0.436353010237;GZF1:-0.444756207773;FOXD3:-0.48534153763;HMGA1,2:-0.496239009071;MEF2{A,B,C,D}:-0.505618440094;MYB:-0.531555659527;ATF2:-0.541061616264;SPIB:-0.579156700121;SOX17:-0.583383167822;ONECUT1,2:-0.600152880297;HOX{A4,D4}:-0.618023537924;VSX1,2:-0.620212977196;NFATC1..3:-0.654746430452;HIC1:-0.656313845493;MAZ:-0.667811651951;PITX1..3:-0.687136875188;ZNF384:-0.698602095813;CUX2:-0.711782439204;ZNF423:-0.723337768119;ZIC1..3:-0.731137112229;RFX1:-0.73130501827;HIF1A:-0.732112432489;NKX2-1,4:-0.737302812399;ELK1,4_GABP{A,B1}:-0.742066363184;SOX2:-0.764429811311;MTF1:-0.768182263802;TGIF1:-0.771157263515;E2F1..5:-0.773504093109;NFY{A,B,C}:-0.779923867536;SOX5:-0.789761093775;PAX2:-0.801872250407;MYBL2:-0.808032939136;AHR_ARNT_ARNT2:-0.80972665618;IKZF2:-0.822453726275;BPTF:-0.827534442322;KLF4:-0.846583973835;FOXL1:-0.850763796015;RREB1:-0.866134664201;LEF1_TCF7_TCF7L1,2:-0.882503071459;TEF:-0.924160442276;ELF1,2,4:-0.950273852624;NHLH1,2:-0.951224046087;PAX6:-0.966314602766;BREu{core}:-0.992167380631;IKZF1:-0.993119080799;MED-1{core}:-0.996039924563;TFAP2B:-1.00136689713;EVI1:-1.00906826927;RORA:-1.01113220918;RFX2..5_RFXANK_RFXAP:-1.03334401474;POU3F1..4:-1.04033931435;ATF4:-1.06812346493;EGR1..3:-1.08639768062;TFAP2{A,C}:-1.10530864406;ZFP161:-1.11493746118;ZBTB16:-1.17459280893;NKX2-2,8:-1.18571410333;SOX{8,9,10}:-1.20127505509;PATZ1:-1.21035403273;MTE{core}:-1.21362397414;FOXP3:-1.31778234792;PRDM1:-1.32980300542;CREB1:-1.33955352014;PAX1,9:-1.37004929681;GLI1..3:-1.41942192832;UFEwm:-1.43882655051;HBP1_HMGB_SSRP1_UBTF:-1.46900837239;MZF1:-1.53812200957;NRF1:-1.54265047518;RXR{A,B,G}:-1.55103190854;HES1:-1.56614612926;FOXP1:-1.61812363039;STAT1,3:-1.64898456311;ALX1:-1.72485310188;TAL1_TCF{3,4,12}:-1.73393560339;STAT5{A,B}:-1.85699468264;HSF1,2:-1.86605739633;EN1,2:-1.88193414788;ZNF143:-1.95809326929;GATA4:-2.1970192659;TFDP1:-2.24498151701;NANOG{mouse}:-2.42201330412;PAX4:-3.06946003303
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:37-13H4;search_select_hide=table117:37-13H4
 }}

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FF:37-13H4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:13, 4 June 2020

CNhs10467

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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