FF:595-22B6

Name:	mammary gland, adult lactating day02
Species:	Mouse (Mus musculus)
Library ID:	CNhs10480
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

ExpandAdditional information
Sample information strain C57BL/6J tissue mammary gland dev stage 2 days lactation adult sex female 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

ExpandCAGE Accession numbers
Method Sample accession id CAGE  SAMD00005704 CollapseLibrary accession numbers Library id Method Exp. accession id Run accession id CNhs10480 CAGE DRX009044 DRR009918 CollapseAccession ID Mm9 Library id BAM CTSS CNhs10480 DRZ001343 DRZ002726 CollapseAccession ID Mm10 Library id BAM CTSS CNhs10480 DRZ012693 DRZ014076

ExpandDownload raw sequence, BAM & CTSS
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Relative expression to median (log10)

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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.

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CAGE peaks	TPM	TF.
p1@Elf5	3.03	1065.16
p2@Elf5	2.66	460.29
p1@Irx2	2.49	467.67
p3@Elf5	2.40	248.83
p1@Bhlha15	1.95	125.40
p2@Irx2	1.87	107.20
p1@Ehf	1.84	107.20
p3@Xbp1	1.78	59.01
p1@Irx1	1.73	79.67
p1@Vdr	1.71	262.11

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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

CNhs10480

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1019	1.954
1041	1.015
1013	0.555
1022	0.394
1000	0.2
1018	0.181
1003	0.16
1039	0.122
1024	0.0865
1032	0.0723
MCL coexpression id	Coexpression_dpi_cluster_scores_median_value

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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

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Repeat family	Log10(Relative expression over median)
ERVL?	2.15
L1,tRNA	0.50
MaLR,MaLR	0.33
Alu,L1	0.27
Simple_repeat,Alu,B4	0.23

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

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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: CNhs10480

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MA0146.1		1.01e-2
MA0114.1		1.04e-1
MA0112.2		1.15e-4
MA0107.1		1.19e-1
MA0144.1		1.20e-4
Jaspar motif	Logo	p-value

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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: CNhs10480

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19		1.05e-1
128		1.14e-2
169		1.15e-3
135		1.19e-1
117		1.26e-1
Novel motif	Logo	p-value

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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: CNhs10480

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011390 mouse mammary gland- adult lactating day02 sample

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0001911 (mammary gland)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002365 (exocrine gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0002330 (exocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000324 (mouse lactating sample)
0011390 (mouse mammary gland- adult lactating day02 sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0008425 (mammary ridge)
UBERON:0010316 (germ layer / neural crest)