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Title:          Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Subject:        Scientific Reports, doi:10.1038/s41598-017-19072-5
Keywords:       
Author:         Yuliaxis Ramayo-Caldas
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     Item: 
      Title: Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed eff ...
      Children: 
       Item: 
        Title: Results and Discussion
        Children: 
         Item: 
          Title: Feed efficiency phenotypes. 
         Item: 
          Title: Mapping and annotation. 
         Item: 
          Title: Genes and biological pathways identified by differential expression analysis between animals with high and low FE. 
         Item: 
          Title: Co-expressed gene modules and correlation with FE traits. 
         Item: 
          Title: Biological pathways deduced from gene modules associated with FE. 
         Item: 
          Title: Identification of candidate genes associated with FE in liver and duodenum tissues. 
         Item: 
          Title: Common genes identified in both liver and duodenum gene modules. 
         Item: 
          Title: Identification of putative master transcriptional factors in the co-expression modules. 
         Item: 
          Title: Common genes and pathways identified in DE and WGCNA analyses. 
       Item: 
        Title: Conclusions
       Item: 
        Title: Material and Methods
        Children: 
         Item: 
          Title: Animals, phenotypes and samples. 
         Item: 
          Title: RNA isolation, library preparation and sequencing. 
         Item: 
          Title: Mapping, assembling and annotation of reads. 
         Item: 
          Title: Differential expression. 
         Item: 
          Title: Validation of differentially-expressed genes by RT-qPCR. 
         Item: 
          Title: Weighted Gene Coexpression Network Analysis (WGCNA). 
         Item: 
          Title: Identification of regulators, functional classification and pathway analyses. 
         Item: 
          Title: Data availability. 
       Item: 
        Title: Acknowledgements
       Item: 
        Title: Figure 1 Gene co-expressed modules identified in liver (A) and duodenum (B), and correlation coefficients (p-values) of each module eigengene with residual feed intake (RFI), residual intake and body weight gain (RIG), and feed conversion ratio (FCR).
       Item: 
        Title: Figure 2 Correlation networks among expression levels of STIP1, HSPA2, HSPA4L, HSPH1, DNAJA1 and DNAJB1 genes in liver and duodenum, and their relationships with residual feed intake (RFI), residual intake and body weight gain (RIG), and feed conversion r
       Item: 
        Title: Table 1 Phenotypic information of analysed animals divergently classified in high and low feed efficiency (FE): mean (standard error) and significance of differences between groups for Residual feed intake (RFI), Feed conversion ratio (FCR), Residual inta
       Item: 
        Title: Table 2 Description of pathways overrepresented in co-expression modules associated to feed efficiency identified in both liver and duodenum tissues.
       Item: 
        Title: Table 3 List of genes in co-expression modules associated to feed efficiency identified in both liver and duodenum tissues.
       Item: 
        Title: Table 4 List of genes associated to feed efficiency commonly identified in a differential expression (DE) and a co-expression network based analyses.
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                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Part of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>part</pdfaProperty:name>
                           <pdfaProperty:valueType>Integer</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Amendment of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>amd</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>conformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://prismstandard.org/namespaces/basic/2.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>prism</pdfaSchema:prefix>
                  <pdfaSchema:schema>Prism</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The aggregation type specifies the unit of aggregation for a content collection. 
Comment 
PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. 
Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. 

</pdfaProperty:description>
                           <pdfaProperty:name>aggregationType</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Copyright </pdfaProperty:description>
                           <pdfaProperty:name>copyright</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The Digital Object Identifier for the article.
The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. 
If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). 
</pdfaProperty:description>
                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>ISSN for an electronic version of the issue in which the resource occurs. 
Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. See prism:issn. 
</pdfaProperty:description>
                           <pdfaProperty:name>issn</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Title of the magazine, or other publication, in which a resource was/will be published. 
Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. 

Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” 
</pdfaProperty:description>
                           <pdfaProperty:name>publicationName</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>This element provides the url for an article or unit of content. 
The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. 
NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. 
</pdfaProperty:description>
                           <pdfaProperty:name>url</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://www.niso.org/schemas/jav/1.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>jav</pdfaSchema:prefix>
                  <pdfaSchema:schema>NISO</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Values for Journal Article Version are one of the following:
AO = Author’s Original
SMUR = Submitted Manuscript Under Review
AM = Accepted Manuscript
P = Proof
VoR = Version of Record
CVoR = Corrected Version of Record
EVoR = Enhanced Version of Record</pdfaProperty:description>
                           <pdfaProperty:name>journal_article_version</pdfaProperty:name>
                           <pdfaProperty:valueType>Closed Choice of Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
            </rdf:Bag>
         </pdfaExtension:schemas>
      </rdf:Description>
   </rdf:RDF>
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