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<FONT SIZE="+1">The following document will help you to find information concerning Gateway-compatible clones and KH transcript models.</FONT>
<p><strong><font size="+1" color="black"><center>
<a href="Access data in Aniseed.pdf">Download the tutorial</a>

</center></font><br>

<FONT SIZE="+3" COLOR="990099"><A NAME="Top"><strong> ANISEED Quick Start </strong><A NAME="Top"></FONT>

<P><FONT SIZE="+2"><strong> Section contents </strong></FONT>

<P><FONT SIZE="+2" COLOR="330099"><strong> The first reflex in ANISEED: <A HREF="#Anisearch">ANISEARCH</A></strong></font>


<P><FONT SIZE="+2" COLOR="330099"><strong> Genes/cDNA clones </strong></font>
<UL TYPE="disc">How do I search for a <A HREF="#Genomicsearch_Gene">gene?</A></UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp What is a "gene" in ANISEED? </UL>
<UL TYPE="disc">How do I search for a <A HREF="#Genomicsearch_GeneModel">gene model?</A></UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp Can you explain the results query ? </UL>
<UL TYPE="disc"> How do I search for a <A HREF="#Genomicsearch_Clone">clone?</A></UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp Can you explain the results query ? </UL>
<UL TYPE="disc">How do I search for a <A HREF="#Genomicsearch_reg_seq">regulatory sequence?</A></UL>
<UL TYPE="disc">How do I search for a gene model by <A HREF="#Genomicsearch_FunctionnalAnnotation">functionnal annotation?</A></UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp I search for gene model using identifier(s) or term(s) of Gene ontology </UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp I search for gene model using identifier(s) or term(s) of Interpro </UL>


<P><FONT SIZE="+2" COLOR="330099"><strong> Explore the genome</strong></font><P>
<UL TYPE="disc"><A HREF="#Blast">Blast search</A></UL>
<UL TYPE="disc">Go to the <A HREF="#Genome_browser">Aniseed genome browser</A></UL>



<P><FONT SIZE="+2" COLOR="330099"><strong> Explore Anatomy </strong></font>
<UL TYPE="disc">How do I find an <A HREF="#Search_anatomy_ontology">anatomical territory in the ontology?</A></UL>
<UL TYPE="disc">How do I find an <A HREF="#Search_anatomy_scheme">anatomical territory on an embryo scheme?</A></UL>
<UL TYPE="disc">How do I find a <A HREF="#Search_territories_fates">territories by their fates?</A></UL>
<UL TYPE="disc">How do I find a <A HREF="#Search_progeny_precursors">progeny/precursors of a territory?</A></UL>
<UL TYPE="disc">How do I find <A HREF="#Search_neighbours">neighbours of a cell?</A></UL>



<P><FONT SIZE="+2" COLOR="330099"><strong> Expression data</em></strong></font>
<UL TYPE="disc">How do I search by <A HREF="#Expressionsearch_by_molecule">molecule ?</A></UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp Can you explain the results query ? </UL>
<UL TYPE="disc">How do I search by <A HREF="#Expressionsearch_by_anatomy">anatomy ?  </A></UL>
<UL TYPE="disc"> &nbsp &nbsp &nbsp Can you explain the results query ? </UL>



<P><FONT SIZE="+2" COLOR="330099"><strong> Explore literature </strong></font>
<UL TYPE="disc"><A HREF="#Keyword_article"> Keyword search into article corpus</A></UL>
<UL TYPE="disc"><A HREF="#Articles_aniseed"> Show all articles present into the database</A></UL>



<P><FONT SIZE="+2" COLOR="330099"><strong> Download </strong></font>
<UL TYPE="disc">Download <A HREF="#Aniseed_data"> Aniseed data</A></UL>
<UL TYPE="disc">Download <A HREF="#3DVE"> 3D Virtual Embryo</A></UL>

<BR>
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<P><FONT SIZE="+2" COLOR="330099"><A NAME="Anisearch"><strong> The first reflex in ANISEED: ANISEARCH</strong></A></font></p>
<IMG SRC="PictureHelp/Anisearch.bmp"><p>
<div align=justify>
Anisearch is a Google-like search engine, which scans all tables of the database for the desired information (this includes comment fields!). You can find Anisearch on the banner page and in the top right corner of each web page.
Just type in the keywords you are interested in and select the "and" and "or" or "complete sentence" operators to link your keywords. The results comes out classified according to various fields (GO term, molecules, ISH comments, articles ) and cross linked to Aniseed and to the genome browser. <p>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find the ISH comments related to "pem".</strong></td></TR>
      </TABLE>
      <p>
      

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<P><FONT SIZE="+2" COLOR="330099"><strong>Genes/cDNA clones</em> </strong></font><p>
<IMG SRC="PictureHelp/GenesMenu.bmp"><p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Genomicsearch_Gene"> How do I search for a gene? </A></FONT><p>

<UL><LI><FONT SIZE="+1" COLOR="CC6633"><EM> What is a "gene" in ANISEED? </A></EM></LI></FONT><P>

<EM>IN PROCESS</EM><P></UL>


<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Genomicsearch_GeneModel"> How do I search for a gene model? </A></FONT><p>

ANISEED supports now three Ciona gene model sets:  JGI v1.0, KyotoGrail 2005 and ENSEMBL. Each of these gene models was functionally annotated either via the Aniseed pipeline (JGI v1.0; Kyotograil2005) or by importing an external functional annotation (ENSEMBL). A single Halocynthia gene set is supported. A biological name is associated to each gene model either by inference from its orthologues in mouse, human, and drosophila or from the best blast hit in Swissprot.
You can search gene models by biological name or ID. <p>

      <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Enter the biological name or the identifier of the gene model (ENSEMBL, JGI v1.0, KYOTOGRAIL2005) you are looking for. </LI><br>
                   <LI>Click on the "Submit" button. <p>

      <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find the sequence of Otx</strong></td></TR>
      </TABLE> </LI></OL>
      <p>
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  <!--    Look at the movie <A HREF="Videoflv/SearchGeneModel.flv"><IMG SRC='PictureHelp/movie_symbol.gif' BORDER="0"></A> or--> click<A HREF="molecule-search.php">here</A> to run this search in ANISEED.<p>

<UL><LI><FONT SIZE="+1" COLOR="CC6633"><EM> Can you explain the result of this query? </A></EM></FONT><P>
The result of your query will be presented in a list of the gene model ID (ENSEMBL, JGI v1.0 or KYOTOGRAIL2005), the associated biological name and the specie. You will also access to the best blast hits records displayed on the gene models found by your query. You can either click on the gene name of interest to get the associated gene model card, or tick right of the gene model ID to constitute a list of genes of interest that can be further restricted using the "Refine" button that enables sequential requests.<p>

<UL><LI> What is it described on a gene model card? </LI><p>
                 This page gives access to the functional annotation (name, scaffold, orthologous in mouse, human and drosophila, best blast hit in Swissprot, interpro domains and Gene Ontology classification), the other tabs give access to the sequence (nucleotide and aa), associated ESTs, EST counts in the various sequenced libraries, in situ data in WT and manipulated conditions, molecular tools (morpholinos, full length Gateway clones), microarray probes (to be implemented). The genomic annotations can be exported as a flat file via the export tab.<p>
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      <A HREF="#Top">Return on the top</A></LI></UL></UL>

<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Genomicsearch_Clone"> How do I search for a clone? </A></FONT><p>
You can search for clone present in ANISEED by clone name.<p>

      <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Enter the name of the clone you are looking for. </LI><br>
                   <LI>Click on the "Submit" button. <p>
      
      <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find In Situ data assossiated to the clone cicl01i06.</strong></td></TR>
      </TABLE> </LI></OL>
      <p>
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     <!-- Look at the movie <A HREF="Videoflv/SearchClone.flv"><IMG SRC='PictureHelp/movie_symbol.gif' BORDER="0"></A> or--> click <A HREF="clone-search.php">here</A> to run this search in ANISEED.<p>

      <UL><LI><FONT SIZE="+1" COLOR="CC6633"><EM>Can you explain the result of this query? </A></EM></FONT></LI><P>
      The "clone" page:<br>

      The result of your query will be presented in a list of the clones found in ANISEED corresponding to the clone name that you search. You can access on the description of the clone by clicking on the link. The corresponding page gives access to some features like the library where the clone came from, the vector used You will also find the different clone sequences corresponding to the clone and the cluster that the clone belongs to from the three assemblies. <p>
      <UL><LI>What is it described on a "clone sequence" page?<p>
      Some features like a brief description, the type of the sequence (EST or cDNA), the orientation are first described. You can also access directly to the Genbank clone card by clicking on the Genbank ID. You retrieve the library used, the vector used, the tissue or the organ that it comes from. There are also the genes models corresponding to the clone sequence and when available, a link to the in situ data. Finally, you can find the sequence.
      All the information of this page can be exported in raw text format by clicking on "Display entry in raw text format".
      </LI><p>
      <LI>What is it described on a "cluster" page?</LI><P>
      Some features like the name of the cluster, the number of the clones present, the corresponding gene and the specie are first described. You will also access to the list of the different clone sequence, with its corresponding clone and its orientation. You can click on each clone name or on each clone sequence to find more details.
A "download" button allows you to export the sequence of all the clone (button "select all") or only of the clone that you are interested in by clicking on the corresponding checked boxe.  
</UL><p>
      
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      <!--Look at the movie <A HREF="Videoflv/ExplainResultGenomicSearchClone.flv"><IMG SRC='PictureHelp/movie_symbol.gif' BORDER="0"></A> or--> click <A HREF="clone-search.php">here</A> to run this search in ANISEED.<p>

      <A HREF="#Top">Return on the top</A><P></UL>

<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Genomicsearch_reg_seq"> How do I search for a regulatory sequence? </A></FONT><p>
<em>In process</em><p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Genomicsearch_FunctionnalAnnotation"> How do I search for a gene model by functionnal annotation? </A></FONT><br>
<FONT SIZE="+1">I search for gene model using identifier(s) or term(s) of Gene ontology</FONT><p>
The Aniseed pipeline annotation forms the basis for the Gene Ontology classifications of the genes. This page allows you to search for genes according to their associated Gene Ontology terms (search for proteins involved in a given process, molecular function, subcellular loicalisation).
After entered terms or identifiers of GO you are looking for, you will have a list a GO terms corresponding to your query. You can Select GO terms of interest, specify the specie that you want the genes and click on "get corresponding gene" button. The GO terms were associated to the gene thanks to the ortholog prediction and/or the best blast hits and/or Interproscan. You can also specify in your query if you only want that the GO terms were predicted with one or all by the "soft".
      The result of this query will give you a list of genes model with the GO terms you have clicked. You can use the refine tool to select specific gene model in the list. <p>
<p>

      <OL TYPE="1"><LI>Enter the term(s) or the identifier(s) of Gene Ontology you are looking for. </LI><br>
                   <LI>Click on the "Submit" button. <p>
      You can enter several terms or identifiers by separating your entries with a space. <p>

      <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find for gene model with a transcription regulator activity </strong></td></TR>
      </TABLE></LI></OL>
      <p>

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      <!--Look at the movie <A HREF="Videoflv/SearchGeneGO.flv"><IMG SRC='PictureHelp/movie_symbol.gif' BORDER="0"></A> or--> click <A HREF="GO-search.php">here</A> to run this search in ANISEED.<p>

      <A HREF="#Top">Return on the top</A><P></LI></UL>

<FONT SIZE="+1">I search for gene model using identifier(s) or term(s) of Interpro</FONT><p>
Interproscan was performed for each Ciona protein and thus, the presence of functional motifs were deduced. You can search for genes according to their InterPro terms (search for protein with given protein motifs).<p>
After entering the term(s) or the identifier(s) of Interpro, you will have a list of Interpro terms corresponding to your query. You can Select Interpro terms of interest, specify the specie that you want the genes and click on "get corresponding gene" button. The result of this query will give you a list of genes model with the Interpro terms you have clicked. You can use the refine tool to select specific gene model in the list.
      
      
      <OL TYPE="1"><LI>Enter the term(s) or the identifier(s) of Interpro you are looking for. </LI><br>
                   <LI>Click on the "Submit" button.<p>
      You can enter several terms or IDs by separating your entries with a space. <p>
      
      <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find for gene model containing homeoboxes </strong></td></TR>
      </TABLE> </LI></OL>
      <p>
      
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      <A HREF="#Top">Return on the top</A><P></LI></UL>
      

<P><FONT SIZE="+2" COLOR="330099"><strong> Explore the genome </em> </strong></font><p>
<IMG SRC="PictureHelp/GenomeMenu.bmp"><p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Blast"> Blast search </A></FONT><p>
<em>In process </em><P>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Genome_Browser"> Go the Aniseed genome browser </A></FONT><p>
<em>In process </em><P>







<P><FONT SIZE="+2" COLOR="330099"><strong> Explore Anatomy </strong></font><p>
<IMG SRC="PictureHelp/AnatomyMenu.bmp"><p>

<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Search_anatomy_ontology">How do I find an anatomical territory in the ontology? </A></FONT><p>
This page allows you to find a territory by searching the anatomical ontology of a species of interest.

      <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><br>
                   <LI>Click on the "Submit" button. </LI><p>

The results page displays the ontology on the left and, depending on the developmental stages, embryo schemes on the right. <p>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find the anatomical dictionary and the scheme of a 64-cell stage embryo.</strong></td></TR>
      </TABLE>
      <p>
</OL>

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<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Search_anatomy_scheme">How do I find an anatomical territory on an embryo scheme? </A></FONT><p>
This page allows to retrieve a territory according to its localisation on embryo schemes. You can search whole Ciona and Halocynthia embryos up to the 110-cell stage and the neural plate of Ciona embryos up to the early tailbud stage. <p>

   <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><br>
                   <LI>Click on the "Submit" button. </LI><p>

The results page displays a clickable embryo scheme.<p>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find what are the little cells localized in the posterior part of a 110-cell stage embryo.</strong></td></TR>
      </TABLE>
      <p>
</OL>

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<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Search_territories_fates">How do I find territories by their fates? </A></FONT><p>

This page allows you to find the territory at a given stage that gives rise to a fate of interest. <p>

      <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><br>
                   <LI>Choose a "Fate" of interest from the menu by clicking on the arrows and scrolling down. </LI><br>
                   <LI>Click on the "Submit" button. </LI><p>

You can select several fates and use the boolean operators on the right of the page to restrict your query. The result page lists the corresponding territories. <P>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find cells at 64-cell stage which give rise only to notochord.</strong></td></TR>
      </TABLE>
      <p>
</OL>

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<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Search_progeny_precursors">How do I find progeny/precursors of a territory? </A></FONT><p>

This page allows you to retrieve from the lineage data the precursors/ progeny of a territory of interest.<P>

      <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><br>
                   <LI>Add territories by clicking on the Add button. A pop up window opens that allows to select territories from the relevant anatomical ontology. You can remove territories or reset the whole field. </LI><br>
                   <LI>Tick on the right whether you want to see the progenitors, progeny or both. </LI><br>
                   <LI>Click on the "Submit" button. </LI><p>

Upon submission of the request the relevant part of the lineage is displayed in a new window.<p>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You want to find progenies and progenitors of B7.6 cell pair.</strong></td></TR>
      </TABLE>
      <p>
</OL>

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<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Search_neighbours">How do I find neighbours of a cell? </A></FONT><p>

This page allows to search 3D Virtual Embryo data to identify the neighbouring territory of a cell, currentlyup to the 44 cell stage of Ciona intestinalis.
      <OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down.</LI><br>
                   <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><br>
                   <LI>Add territories by clicking on the Add button. A pop up window opens that allows to select territories from the relevant anatomical ontology. You can remove territories or reset the whole field. </LI><br>
                   <LI>You can change the default maximum distance to neighbouring territory (<5m). </LI><br>
                   <LI>You can change the default surface of contact between cells (>0m). </LI><br>
                   <LI>Click on the "Submit" button. </LI><p>

Upon submission, a new page appears listing the neighbouring structures and the surface of contact with the territory of interest.<P>

<TABLE background="CC00CC" border="3" width="40%">
             <TR> <td><strong>Example <p> </strong></td></TR>
             <TR> <td><strong>You want to identify the neighbouring territory of a4.2.</strong></td></TR>
      </TABLE>
      <p>
</OL>

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<P><FONT SIZE="+2" COLOR="330099"><strong> Expression data </strong></font><p>
<IMG SRC="PictureHelp/ExpressionMenu.bmp"><p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Expressionsearch_by_molecule"> How do I search by molecule ? </A></FONT><p>
This page allows you to find the in situ expression patterns associated to a gene or EST/cDNA clone. By default only the wild type expression patterns are shown but you can access expression patterns in manipulated conditions (gene deregulation, embryo manipulation) by ticking/filling the relevant boxes/fields. <p>

<OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down. </LI><BR>
             <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><BR>
             <LI>Enter the clone or the gene model of interest in the "stained molecule" box. If you don't know the ID of the gene model, you can search your molecule ID using the "Find a gene model by its name" interface. You can enter several molecules separated by ":". <EM> If you click on the "and" button, the result will give you all the ISH stained with the several molecules you have entered. If you click on the "or" button, you will have all the ISH stained with one or the others molecules</LI></EM><p>

             <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search for wild type expression data of Otx.</strong></td></TR>
      </TABLE>
      <p>

      Look at the movie <A HREF="Videoflv/HSHSearch_otx2.flv"><IMG SRC='PictureHelp/movie_symbol.gif' BORDER="0"></A> 

            <LI>If you just want to access expression pattern in manipulated conditions like gene deregulation, click on the corresponding "any" button. You can specify by entering a gene model ID in the corresponding box, a gene which could be deregulated in an experiment. Moreover, like the stained molecule, you can enter several gene models ID separated by ":" and use the "and" and "or" button.</LI><p>

            <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search for expression data of Snail in which Nodal was downregulated.</strong></td></TR>
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      <p>
             <LI>If you just want to access expression pattern in manipulated conditions like embryo manipulation, click on the corresponding "any" button. You can include (with the "include" button), these manipulated conditions in others complex queries.</LI><p>

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             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search for expression data of Snail in which the b6-5 blastomere was ablated on the right side at the 32-cell stage.</strong></td></TR>
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             <LI>You can also restrict your search to the in situ experiments from a given author or found in a paper identified by its Pubmed ID by filling the relevant fields.</LI><p>

             <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search for expression data of Snail made by Clare Hudson.</strong></td></TR>
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            <LI>Finally, you can order the results according to the developmental stages or according to the species.</LI><p>
      </OL>

      <UL><LI><FONT SIZE="+1" COLOR="CC6633"><EM>Can you explain the result of this query? </A></EM></FONT><P>
      You will have a list of all the experiment data corresponding to your query ordered by developmental stages (default option). The number of the experiment is specified on the top right of the window. You can click on the top left of the window to zoom in or to zoom out the pictures. At the bottom, you will access to the refine tool. If you want to know more about an experiment, you can click on the corresponding "more" button.<p>

               </LI></UL>


<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Expressionsearch_by_anatomy"> How do I search by anatomy ? </A></FONT><p>
This page allows you to retrieve In situ expression profiles labelling defined territories, and excluded from others. By default only the wild type expression patterns are shown but you can access expression patterns in manipulated conditions (gene deregulation, embryo manipulation) by ticking/filling the relevant boxes/fields.<p>
<OL TYPE="1"><LI>Choose an "Ascidian species" from the menu by clicking on the arrows and scrolling down. </LI><BR>
             <LI>Choose a "Developmental stage" from the menu by clicking on the arrows and scrolling down. </LI><BR>
             <LI>Define you territories of interest either via the detailed anatomical ontology for each stage (use the "Add" button) or a simpler list of fates. To find tissue specific expression patterns tick the "only" box.</LI><BR>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search for the genes only expressed in B7.6 at 110 cell stage.</strong></td></TR>
      </TABLE>
      <p>

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            <LI>You can also specify that you want to exclude patterns labelling a list of unwanted territories.</LI><br>

<TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search for the genes expressed in the endodermal strand and not in muscles.</strong></td></TR>
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</OL>


<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Expressionsearch_by_article"> How do I search by article ? </A></FONT><p>

      <OL TYPE="1"><LI>Identify the PubmedID of the article you want to search.</LI><br>
                   <LI>Enter the PubmedID in the search box. </LI><br>
                   <LI>Click on the "Submit" button. <p>
      


      <TABLE background="CC00CC" border="3" width="40%">
             <TR ALIGN="center"> <td><strong>Example <p> </strong></td></TR>
             <TR ALIGN="center"> <td><strong>You search the expression data corresponding to the article "Regulatory blueprint for a chordate embryo".<br> The pubmedID of this article is 16728634 </strong></td></TR>
      </TABLE> </LI></OL>
      


<P><FONT SIZE="+2" COLOR="330099"><strong> Explore Literature </strong></font>
<p><IMG SRC="PictureHelp/LiteratureMenu.bmp"><p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Keyword_article"> Keyword search into articles corpus  </A></FONT><p>
<em>In process</em> <p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Articles_aniseed"> Show all articles present into the database </A></FONT><p>
<em>In process</em> <p>


<P><FONT SIZE="+2" COLOR="330099"><strong> Explore Literature </strong></font>
<p><IMG SRC="PictureHelp/DownloadMenu.bmp"><p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="Aniseed_data"> Download Aniseed data </A></FONT><p>
<em>In process</em> <p>
<FONT SIZE="+1" COLOR="CC00CC"><A NAME="3DVE"> Download 3D Virtual Embryo </A></FONT><p>
<em>In process</em> <p>


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