Rdf-0607
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@prefix : <http://purl.org/net/biordfmicroarray/ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix ex: <http://purl.org/net/biordfmicroarray/ns#> .
@prefix ss: <http://purl.org/net/biordfmicroarray/ns#> .
@prefix biordf: <http://purl.org/net/biordfmicroarray/id/> .
@prefix genbank: <http://bio2rdf.org/affymetrix:> .
@prefix stat: <http://purl.org/net/biordfmicroarray/ns#> .
##### gene list 1 (http://public.tgen.org/tgen.org/supplementarydata/neurogenomics/supplementarydata/dunckley_etal/U133_plus_2.0_AD.xls)
##genelist 1 goes from gene1 through gene262 - keeping those in a separate file
##### revised on April 23, to replace "geneexpression" with "expression"
ex:gene1 :probe_set_id "225871_at" ;
:name "six transmembrane epithelial antigen of prostate 2" ;
rdfs:label "STEAP2" ;
rdf:type :gene ;
:expressed_in ex:sample_list1 .
ex:gene2 :probe_set_id "225621_at" ;
:name "GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransferase" ;
rdfs:label "ALG2" ;
rdf:type :gene ;
:expressed_in ex:sample_list1 .
ex:signal1
rdf:type :signal ;
rdf:value "343.9" .
ex:detection1
rdf:type :detection ;
rdf:value "A" .
ex:sample1
:derives_from biordf:Entorhinal_cortex ;
:derives_from biordf:human ;
rdfs:label "AD tangle 1" ;
rdf:type :sample .
ex:experiment1
:has_input_value ex:sample1 ;
:has_input_value ex:gene1 ;
:has_output_value ex:signal1 ;
:has_output_value ex:detection1 .
biordf:human
:has_disease_state biordf:Alzheimers_disease ;
rdf:type :Human .
##Added 20100607 to represent fold change and p-value associated with a microarray experiment
ex:microarray_experiment_set1
rdfs:member ex:experiment1 ;
:diff_expressed_gene ex:gene1 ;
:has_ouput_value ex:fold_change1 .
ex:fold_change1
rdf:value "0.6183" ;
stat:p_value "0.000016" .
######## gene list 2 (http://public.tgen.org/tgen.org/supplementarydata/neurogenomics/supplementarydata/brain_regions/PCA1_0_98_correlation.xls)
##genelist2 goes from gene 263 through gene 364 - see separate file with all the genes for genelist2
ex:gene263
:probe_set_id "1556743_at" ;
:genbank_id "AI732587" ;
rdf:type :gene ;
:expressed_in ex:sample_list2 ;
:expressed_in ex:sample_list3 ;
:expressed_in ex:sample_list4 ;
:expressed_in ex:sample_list5 ;
:expressed_in ex:sample_list6 ;
:expressed_in ex:sample_list7 .
ex:gene264
:probe_set_id "1557098_s_at" ;
:genbank_id "AW593432" ;
:name "CDNA clone IMAGE:4812795" ;
rdf:type :gene ;
:expressed_in ex:sample_list2 ;
:expressed_in ex:sample_list3 ;
:expressed_in ex:sample_list4 ;
:expressed_in ex:sample_list5 ;
:expressed_in ex:sample_list6 ;
:expressed_in ex:sample_list7 .
ex:gene265
:probe_set_id "1557118_a_at" ;
:genbank_id "AW236954" ;
:name "CDNA clone IMAGE:4812643" ;
rdf:type :gene ;
:expressed_in ex:sample_list2 ;
:expressed_in ex:sample_list3 ;
:expressed_in ex:sample_list4 ;
:expressed_in ex:sample_list5 ;
:expressed_in ex:sample_list6 ;
:expressed_in ex:sample_list7 .
ex:gene266
:probe_set_id "1558724_at" ;
:genbank_id "BM805933" ;
:name "Hypothetical protein LOC645478" ;
rdfs:label "LOC645478" ;
rdf:type :gene ;
:expressed_in ex:sample_list2 ;
:expressed_in ex:sample_list3 ;
:expressed_in ex:sample_list4 ;
:expressed_in ex:sample_list5 ;
:expressed_in ex:sample_list6 ;
:expressed_in ex:sample_list7 .
ex:sample_list2
:derives_from biordf:Entorhinal_cortex .
ex:sample_list3
:derives_from biordf:Hippocampus .
ex:sample_list4
:derives_from biordf:Middle_temporal_gyrus .
ex:sample_list5
:derives_from biordf:Posterior_cingulate_cortex .
ex:sample_list6
:derives_from biordf:Superior_frontal_gyrus.
ex:sample_list7
:derives_from biordf:primary_visual_cortex.
ex:experiment2
:has_input_value ex:sample_list2 ;
:has_input_value ex:gene2 ;
:has_output_value ex:avg_signal1 .
ex:avg_signal1 rdf:type :signal ;
rdf:value "75.34285714" .
ex:microarray_experiment_set2
rdfs:member ex:experiment2 ;
:diff_expressed_gene ex:gene263 .
##genelist 3
ex:gene365
:probe_set_id "1569891_at" ;
rdfs:label "ATP5A1" ;
:genbank_id "BC035703" ;
rdf:type :gene ;
:expressed_in ex:sample_list8 ;
:expressed_in ex:sample_list9 ;
:expressed_in ex:sample_list10 ;
:expressed_in ex:sample_list11 ;
:expressed_in ex:sample_list12 ;
:expressed_in ex:sample_list13 .
ex:gene366
:probe_set_id "213738_s_at" ;
rdfs:label "ATP5A1" ;
:genbank_id "AI587323" ;
rdf:type :gene ;
:expressed_in ex:sample_list8 ;
:expressed_in ex:sample_list9 ;
:expressed_in ex:sample_list10 ;
:expressed_in ex:sample_list11 ;
:expressed_in ex:sample_list12 ;
:expressed_in ex:sample_list13 .
ex:gene367
:probe_set_id "201322_at" ;
rdfs:label "ATP5B" ;
:genbank_id "NM_001686" ;
rdf:type :gene ;
:expressed_in ex:sample_list8 ;
:expressed_in ex:sample_list9 ;
:expressed_in ex:sample_list10 ;
:expressed_in ex:sample_list11 ;
:expressed_in ex:sample_list12 ;
:expressed_in ex:sample_list13 .
:sample_list8
:derives_from biordf:Posterior_cingulate_cortex .
:sample_list9
:derives_from biordf:Middle_temporal_gyrus .
:sample_list10
:derives_from biordf:Hippocampus .
:sample_list11
:derives_from biordf:Entorhinal_cortex .
:sample_list12
:derives_from biordf:Primary_visual_cortex .
:sample_list13
:derives_from biordf:Superior_frontal_gyrus .
ex:microarray_experiment_set3
:has_sample_list ex:sample_list8 ;
:diff_expressed_gene ex:gene366 ;
:has_ouput_value ex:fold_change366 .
ex:fold_change366
rdf:value "-4.35782" ;
stat:p_value "2.62880*10^-7" ;
stat:corrected_p_value "2.6313*10^-7" .
