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" .