Personal tools

FF:59-29C1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:59-29C1 |name=submandibular gland, adult, biol_rep1 |sample_id=59 |rna_tube_id=59-29C1 |rna_box=59-29C1 |rna_position=59-29C1 |sample_cell_lot= |sam...")
 
No edit summary
Line 40: Line 40:
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|sample_description=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 66:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=bHLH_family:2.25156604815;FOXO1,3,4:2.21532691275;ATF6:2.21414494343;ALX1:2.18535278559;HAND1,2:2.1003865343;SNAI1..3:1.97962697295;TLX2:1.8855644112;ZEB1:1.69509924473;IRF7:1.55364747699;FOXQ1:1.5075396107;DMAP1_NCOR{1,2}_SMARC:1.49968179328;AR:1.30523994486;TP53:1.26324201346;POU2F1..3:1.22141484014;IRF1,2:0.964264841371;HIF1A:0.909510738727;ESRRA:0.896325300567;HMX1:0.861989172758;MYOD1:0.854494320147;FOXN1:0.850968670012;PAX1,9:0.75631483177;ETS1,2:0.754941205772;NFIX:0.749909384682;TEF:0.702747230169;TGIF1:0.680285652457;SP1:0.633281051965;NR1H4:0.628948518442;FOXP1:0.605216390374;XCPE1{core}:0.576078935426;HBP1_HMGB_SSRP1_UBTF:0.557498853569;SOX5:0.504005372734;LMO2:0.500386297072;ELF1,2,4:0.497527817777;ESR1:0.482468295859;DBP:0.440759305347;SPZ1:0.439813976853;FOX{D1,D2}:0.419671823365;SPIB:0.399161329776;MAFB:0.380176646938;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.378747550438;FOX{I1,J2}:0.361702452053;RUNX1..3:0.348339637292;PPARG:0.34044905856;SPI1:0.218763336517;CEBPA,B_DDIT3:0.211622437224;NFIL3:0.201724662168;MYBL2:0.165735099669;NANOG:0.134120191661;T:0.129031861783;GZF1:0.105521627411;NFATC1..3:0.0922433972573;ZBTB16:0.0872336410541;PAX4:0.0761386697432;STAT2,4,6:0.0720445265737;LHX3,4:0.068989712752;TFAP2{A,C}:0.0679886390655;TFAP4:0.0614994173314;NR6A1:0.0381291131544;REST:0.0193426482966;FOS_FOS{B,L1}_JUN{B,D}:0.0125044107009;SREBF1,2:0.0073891287437;NFKB1_REL_RELA:0.00416297896268;FOXM1:0.00174652617123;ADNP_IRX_SIX_ZHX:-0.00194251357932;GLI1..3:-0.00414123125327;FOXA2:-0.00414853896831;AIRE:-0.0219077120655;ATF2:-0.0269209597237;SRF:-0.106523087532;TEAD1:-0.115047791318;NHLH1,2:-0.130639336202;TBP:-0.138105630666;GTF2A1,2:-0.151805680559;PAX6:-0.158454998065;POU5F1:-0.160355232097;CREB1:-0.17388897593;HIC1:-0.19587369831;BPTF:-0.217265222779;NR5A1,2:-0.222517532249;CRX:-0.227281062795;STAT5{A,B}:-0.239532270756;GTF2I:-0.242609415534;ZNF148:-0.243242906762;ARID5B:-0.243564970516;PRDM1:-0.249422745871;MEF2{A,B,C,D}:-0.269136340598;NFE2L2:-0.271212961171;GCM1,2:-0.278875790051;NKX2-1,4:-0.294463444958;TFCP2:-0.300752789211;ELK1,4_GABP{A,B1}:-0.309187567698;TBX4,5:-0.310983425447;ATF5_CREB3:-0.327811079598;EP300:-0.345892547379;AHR_ARNT_ARNT2:-0.358507124249;TLX1..3_NFIC{dimer}:-0.363498158344;IKZF2:-0.366380804962;GATA4:-0.367610572311;ZNF143:-0.414108520597;MED-1{core}:-0.4144762341;OCT4_SOX2{dimer}:-0.416340327552;FOSL2:-0.417007901194;CDC5L:-0.423549406295;FOX{F1,F2,J1}:-0.423886807164;TFAP2B:-0.426523171731;HNF4A_NR2F1,2:-0.427606445533;RXRA_VDR{dimer}:-0.429239450784;FOXP3:-0.444394439562;SOX2:-0.463839514787;MYFfamily:-0.468302071007;HOXA9_MEIS1:-0.479203831943;MTF1:-0.492708825044;ZFP161:-0.497377137557;VSX1,2:-0.508527990494;BACH2:-0.512827273793;MTE{core}:-0.52290244608;NKX2-3_NKX2-5:-0.556143768129;PRRX1,2:-0.568600453746;JUN:-0.594638162582;HNF1A:-0.599644723217;GFI1:-0.602308129346;HMGA1,2:-0.603429365127;HOX{A4,D4}:-0.607907039729;POU6F1:-0.611928659423;SOX{8,9,10}:-0.614084677995;KLF4:-0.615251944119;SMAD1..7,9:-0.618253834085;NFE2L1:-0.636567105924;YY1:-0.644617074285;RFX2..5_RFXANK_RFXAP:-0.645625475973;TOPORS:-0.671595963815;RREB1:-0.671783575884;ZBTB6:-0.674046572804;POU3F1..4:-0.678539648002;NR3C1:-0.683671697317;RXR{A,B,G}:-0.69432912332;MAZ:-0.714629353659;BREu{core}:-0.723545290923;MZF1:-0.725576572297;ZNF384:-0.726713033873;FOXD3:-0.739221374773;MYB:-0.741583465574;HES1:-0.741886728065;NKX3-1:-0.750493958566;HLF:-0.759248497162;EBF1:-0.773562382382;PATZ1:-0.799839276117;RFX1:-0.803643255456;PDX1:-0.81032000792;PITX1..3:-0.821072999033;NANOG{mouse}:-0.851744965605;NRF1:-0.855666573823;GATA6:-0.857093344258;TAL1_TCF{3,4,12}:-0.861100118872;ATF4:-0.886907465347;ALX4:-0.893474819601;IKZF1:-0.937479198519;NKX6-1,2:-0.951312594015;RORA:-0.956076378782;NKX2-2,8:-0.962067026632;CDX1,2,4:-0.969509851794;PAX5:-0.975249006225;CUX2:-0.979321694116;PBX1:-1.01469801757;RBPJ:-1.05275088017;PAX2:-1.06885970668;SOX17:-1.07770760985;NFE2:-1.10136609571;POU1F1:-1.1028293371;EGR1..3:-1.11579810408;NKX3-2:-1.13180141913;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.13297427731;ONECUT1,2:-1.1489001136;NFY{A,B,C}:-1.16385414168;TFDP1:-1.19667500279;GFI1B:-1.19870026798;ZNF238:-1.21865785038;LEF1_TCF7_TCF7L1,2:-1.28909215103;E2F1..5:-1.29140751697;HOX{A5,B5}:-1.31562984483;EN1,2:-1.31995121552;UFEwm:-1.32575155526;EVI1:-1.33648886904;ZIC1..3:-1.48191610795;PAX8:-1.64159032757;FOXL1:-1.87139905138;STAT1,3:-1.92336696018;HSF1,2:-2.04425152795;ZNF423:-2.49011745673
}}
}}

Revision as of 15:21, 15 February 2012


Name:submandibular gland, adult, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuesubmandibular gland
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
CollapseMm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
CollapseMm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10469



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


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: CNhs10469



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: CNhs10469



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: CNhs10469


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000167 (oral cavity)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001044 (saliva-secreting gland)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001736 (submandibular gland)
0001829 (major salivary gland)
0002050 (embryonic structure)
0002330 (exocrine system)
0002365 (exocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003293 (gland of oral region)
0003294 (gland of foregut)
0003408 (gland of gut)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0006298 (submandibular gland primordium)
0007023 (adult organism)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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