FF:1310-23B1

Name:	epididymis and seminiferous tubule, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

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Sample information strain C57BL/6J tissue epididymis and seminiferous tubule dev stage 0 day neonate 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

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CollapseMm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] CollapseMm10 BAM CTSS [{{{mm10bam}}} download] [{{{mm10ctss}}} donwload]

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@Tcf21	2.02	265.50
p1@Osr2	1.69	116.50
p1@Wt1	1.60	60.49
p1@Hoxc6	1.57	36.46
p1@Hoxa10	1.49	29.84
p1@Arx	1.46	34.42
p1@Emx2	1.44	32.38
p2@Wt1	1.35	21.18
p1@Gata2	1.33	164.37
p12@Zbtb20	1.31	19.35

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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

CNhs11218

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1002	0.85
1031	0.701
103	0.671
1014	0.502
1016	0.427
1009	0.331
1040	0.31
1004	0.305
1029	0.226
1003	0.188
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 no result for this sample

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: CNhs11218

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MA0115.1		1.01e-4
MA0079.2		1.10e-1
MA0083.1		1.13e-3
MA0025.1		1.15e-1
MA0140.1		1.20e-2
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: CNhs11218

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135		1.06e-1
114		1.06e-2
166		1.08e-2
80		1.11e-1
95		1.12e-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: CNhs11218

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011506 mouse epididymis and seminiferous tubule- neonate N00 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)
0000922 (embryo)
0002113 (kidney)
0000473 (testis)
0002100 (trunk)
0000483 (epithelium)
0000991 (gonad)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0000990 (reproductive system)
0003914 (epithelial tube)
0005103 (mesonephric epithelium)
0000083 (mesonephric tubule)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0003135 (male reproductive organ)
0000119 (cell layer)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0003133 (reproductive organ)
0004175 (internal genitalia)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0009201 (nephric duct)
0005256 (trunk mesenchyme)
0001048 (primordium)
0003918 (kidney mesenchyme)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0004819 (kidney epithelium)
0004910 (epithelium of male gonad)
0004909 (epithelium of gonad)
0004176 (external genitalia)
0005173 (abdominal segment element)
0005154 (epithelial cord)
0005295 (sex cord)
0002532 (epiblast (generic))
0006553 (renal duct)
0001008 (renal system)
0003101 (male organism)
0003074 (mesonephric duct)
0004122 (genitourinary system)
0000079 (male reproductive system)
0002417 (abdominal segment of trunk)
0006947 (male genital duct)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0004054 (internal male genitalia)
0003064 (intermediate mesoderm)
0004875 (nephrogenic cord)
0009196 (indifferent external genitalia)
0009117 (indifferent gonad)
0004871 (somatic layer of lateral plate mesoderm)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0005564 (gonad primordium)
0005297 (testis sex cord)
0004872 (splanchnic layer of lateral plate mesoderm)
0005095 (kidney rudiment)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0003060 (pronephric duct)
0007687 (kidney field)
0005294 (genital ridge)
0010141 (primitive sex cord of indifferent gonad)
0007297 (presumptive pronephric mesoderm)
0005891 (coelomic epithelium)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA