http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&feed=atom&action=history
M2BBS GDNS-APG - Revision history
2024-03-29T05:51:11Z
Revision history for this page on the wiki
MediaWiki 1.15.1
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=9372&oldid=prev
Barriot at 05:20, 13 October 2022
2022-10-13T05:20:21Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''Ressources''' → Diapos [[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|PDF]] - [https://docs.google.com/presentation/d/1e4dON5UP7rpXi-Un0i6QwXA874hmvUALkNdqzjKWgdk/edit?usp=sharing online] <del class="diffchange diffchange-inline">de cours</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Ressources''' → Diapos <ins class="diffchange diffchange-inline">de cours </ins>[[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|PDF]] - [https://docs.google.com/presentation/d/1e4dON5UP7rpXi-Un0i6QwXA874hmvUALkNdqzjKWgdk/edit?usp=sharing online]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/gdns-ap/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/gdns-ap/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=9371&oldid=prev
Barriot at 05:19, 13 October 2022
2022-10-13T05:19:54Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''Ressources''' → [[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|<del class="diffchange diffchange-inline">Diapos </del>PDF]] - [https://docs.google.com/presentation/d/1e4dON5UP7rpXi-Un0i6QwXA874hmvUALkNdqzjKWgdk/edit?usp=sharing online] de cours</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Ressources''' → <ins class="diffchange diffchange-inline">Diapos </ins>[[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|PDF]] - [https://docs.google.com/presentation/d/1e4dON5UP7rpXi-Un0i6QwXA874hmvUALkNdqzjKWgdk/edit?usp=sharing online] de cours</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/gdns-ap/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/gdns-ap/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=9370&oldid=prev
Barriot at 05:19, 13 October 2022
2022-10-13T05:19:27Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/gdns-ap/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/gdns-ap/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=9369&oldid=prev
Barriot at 12:29, 12 October 2022
2022-10-12T12:29:13Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Projet''' → [[M2BBS_GDNS-APG_-_Projets|Page dédiée]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Projet''' → [[M2BBS_GDNS-APG_-_Projets|Page dédiée]]</div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=9366&oldid=prev
Barriot at 16:47, 11 October 2022
2022-10-11T16:47:28Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Ressources''' → [[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|Diapos]] de cours</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Ressources''' → [[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|Diapos]] de cours</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/<del class="diffchange diffchange-inline">idh/2021</del>/GDNS-APG.Mise.en.oeuvre<del class="diffchange diffchange-inline">.nb</del>.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/<ins class="diffchange diffchange-inline">gdns-ap</ins>/GDNS-APG.Mise.en.oeuvre.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=8692&oldid=prev
Barriot at 09:24, 26 October 2021
2021-10-26T09:24:39Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/idh/2021/GDNS-APG.Mise.en.oeuvre.nb.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Mise en oeuvre''' → [[silico:enseignement/m2bbs/idh/2021/GDNS-APG.Mise.en.oeuvre.nb.html|Notebook]] Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=8554&oldid=prev
Barriot at 13:20, 15 October 2021
2021-10-15T13:20:13Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">= </del>Ressources <del class="diffchange diffchange-inline">=</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''</ins>Ressources<ins class="diffchange diffchange-inline">''' → [Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|Diapos]] de cours</ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">* </del>[[<del class="diffchange diffchange-inline">Media</del>:<del class="diffchange diffchange-inline">M2BBS</del>-<del class="diffchange diffchange-inline">Gestion de donnees non structurees - Applications post-genomiques</del>.<del class="diffchange diffchange-inline">pdf</del>|<del class="diffchange diffchange-inline">Diapos</del>]] <del class="diffchange diffchange-inline">de cours</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''Mise en oeuvre''' → </ins>[[<ins class="diffchange diffchange-inline">silico</ins>:<ins class="diffchange diffchange-inline">enseignement/m2bbs/idh/2021/GDNS</ins>-<ins class="diffchange diffchange-inline">APG</ins>.<ins class="diffchange diffchange-inline">Mise.en.oeuvre.nb.html</ins>|<ins class="diffchange diffchange-inline">Notebook</ins>]] <ins class="diffchange diffchange-inline">Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.</ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">= Mise en oeuvre = </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''Projet''' → [[M2BBS_GDNS-APG_-_Projets|Page dédiée]]</ins></div></td></tr>
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Barriot
http://www.m2p-bioinfo.ups-tlse.fr/site/index.php?title=M2BBS_GDNS-APG&diff=8379&oldid=prev
Barriot at 19:15, 10 October 2021
2021-10-10T19:15:51Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Approche par ensemble : Enrichissement ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Approche par ensemble : Enrichissement ==</div></td></tr>
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Barriot
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Barriot: Created page with '= Ressources = * Diapos de cours = Mise en oeuvre = Illustration sur un organisme. Const…'
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* [[Media:M2BBS-Gestion de donnees non structurees - Applications post-genomiques.pdf|Diapos]] de cours<br />
<br />
= Mise en oeuvre = <br />
<br />
Illustration sur un organisme. Constitution d'une base dédiée à un organisme et son exploitation.<br />
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== Approche par ensemble : Enrichissement ==<br />
<br />
Il a été identifié un ou quelques ensembles de gènes d'intérêt chez ''E. coli''. A quels processus biologiques, fonctions moléculaires ou localisations sub-cellulaires peut-on les relier ?<br />
<br />
Ensembles :<br />
<br />
Utiliser l'interface Web http://silico.biotoul.fr/enrichment/ afin d'analyser ces ensembles.<br />
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=== Ensembles cibles et script de recherche d'enrichissement ===<br />
Un premier exercice, relativement simple, va être de reproduire ce type d'analyse. Nous allons utiliser les mots-clés associer aux protéines dans UniProt.<br />
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==== Génération des ensembles cibles ====<br />
<br />
Aller sur [https://www.uniprot.org UniProt] et télécharger le protéome correspondant à ''E. coli'' K-12 MG1655 ; étapes :<br/><br />
→ sélectionner ''Proteomes'' puis rechercher ''E. coli'' K-12 MG1655. Identifier le bon résultat et cliquer sur son ''Proteome ID''<br/><br />
→ Cliquer ensuite sur ''View all proteins''<br/><br />
→ Dans l'onglet ''Columns'', sélectionner celles que nous allons utiliser par la suite : ''Entry name'', ''Gene names (ordered locus)'', ''Gene Ontology IDs'', ''Interpro''<br/><br />
→ Puis télécharger au format ''Tab-separated''<br />
<br />
Pour générer un fichier texte au format simple qui donne pour chaque mot-clé, la liste des protéines associées, nous allons utiliser R et les librairies ''tidyverse'' et ''jsonlite''.<br />
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===== Choix des identifiants de référence =====<br />
<br />
Un des problèmes souvent rencontrés dans ce type d'analyse est d'arriver à identifier : les génomes et les gènes, protéines, ''etc.'' En effet, chaque source de données peut utiliser des méthodes de référencement et d'identification qui lui est propre. Pour le protéome d'''E. coli'', nous allons utiliser un type d'identifiant très souvent utilisé : les ''bnumbers''.<br />
<br />
A partir du fichier télécharger, vous allez donc le charger sous R et le reformater pour avoir un ''mapping'' des identifiants UniProt vers les ''bnumbers''.<br />
<br />
<source lang='rsplus'><br />
library(tidyverse)<br />
uniprot = read_tsv("uniprot/uniprot-proteome_UP000000625.tab")<br />
uniprot<br />
</source><br />
<pre><br />
# A tibble: 4,438 x 6<br />
Entry `Entry name` `Gene names (orde… `Gene ontology IDs` Keywords `Cross-reference (InterPro…<br />
<chr> <chr> <chr> <chr> <chr> <chr> <br />
1 P0AAG8 MGLA_ECOLI b2149 JW2136 GO:0005354; GO:0005524; GO:0005886; GO… ATP-binding;Cell inner membran… IPR003593;IPR003439;IPR017…<br />
2 P0A749 MURA_ECOLI b3189 JW3156 GO:0005829; GO:0007049; GO:0008360; GO… 3D-structure;Cell cycle;Cell d… IPR001986;IPR036968;IPR013…<br />
3 P77737 OPPF_ECOLI b1247 JW1239 GO:0005524; GO:0005886; GO:0015031; GO… ATP-binding;Cell inner membran… IPR003593;IPR003439;IPR017…<br />
4 P23837 PHOQ_ECOLI b1129 JW1115 GO:0000155; GO:0000160; GO:0004721; GO… 3D-structure;ATP-binding;Cell … IPR003660;IPR003594;IPR036…<br />
5 P23865 PRC_ECOLI b1830 JW1819 GO:0004175; GO:0004252; GO:0005886; GO… 3D-structure;Cell inner membra… IPR029045;IPR001478;IPR036…<br />
6 P32155 PTFLA_ECOLI b3900 JW3871 GO:0005737; GO:0008982; GO:0009401; GO… Cytoplasm;Kinase;Phosphoprotei… IPR016152;IPR002178;IPR004…<br />
7 P69801 PTNC_ECOLI b1818 JW1807 GO:0005886; GO:0005887; GO:0009401; GO… 3D-structure;Cell inner membra… IPR004700; <br />
8 P65870 QUED_ECOLI b2765 JW2735 GO:0008270; GO:0008616; GO:0042802; GO… 3D-structure;Lyase;Metal-bindi… IPR007115;IPR038418; <br />
9 P0AAZ4 RARA_ECOLI b0892 JW0875 GO:0003677; GO:0005524; GO:0006261; GO… 3D-structure;ATP-binding;DNA r… IPR003593;IPR032423;IPR003…<br />
10 P0A7R1 RL9_ECOLI b4203 JW4161 GO:0003735; GO:0005829; GO:0006412; GO… 3D-structure;Acetylation;Direc… IPR000244;IPR009027;IPR020…<br />
# … with 4,428 more rows<br />
</pre><br />
<br />
A partir de ce ''tibble'', il s'agit d'extraire les ''bnumbers'' de la colonne ''Gene names (ordered locus)''. La fonction ''str_extract'' permet d'extraire un ''pattern'' à partir d'une expression régulière (ici ce sera <tt>'b\\d+'</tt>) d'une chaîne de caractères. Le résultat devrait correspondre à :<br />
<source lang='rsplus'><br />
mapping<br />
</source><br />
<pre><br />
# A tibble: 4,436 x 2<br />
bnumber uniprotID<br />
<chr> <chr> <br />
1 b0001 P0AD86 <br />
2 b0002 P00561 <br />
3 b0003 P00547 <br />
4 b0004 P00934 <br />
5 b0005 P75616 <br />
6 b0006 P0A8I3 <br />
7 b0007 P30143 <br />
8 b0008 P0A870 <br />
9 b0009 P0AF03 <br />
10 b0010 P0AC98 <br />
# … with 4,426 more rows</pre><br />
<br />
===== Reformatage des données =====<br />
<br />
A présent, il s'agit de générer la liste des protéines associées à chaque mot-clé (colonne ''Keywords''). Pour cela, on ne gardera que les colonnes ''Entry'' et ''Keywords'', une jointure avec ''mapping'' va permettre de faire le mapping avec les ''bnumbers''. La fonction ''separate_rows'' va nous servir à découper la colonne ''Keywords'' et répartir les mots-clés sur des lignes du tibble :<br />
<source lang='rsplus'><br />
keywords = uniprot %>% <br />
select(uniprotID=Entry, keyword=Keywords) %>%<br />
right_join(mapping) %>% # right join to remove those without bnumber<br />
separate_rows(keyword, sep=';') %>%<br />
select(bnumber, keyword) %>%<br />
arrange(bnumber)<br />
keywords<br />
</source><br />
<pre><br />
# A tibble: 27,308 x 2<br />
bnumber keyword <br />
<chr> <chr> <br />
1 b0001 Amino-acid biosynthesis <br />
2 b0001 Leader peptide <br />
3 b0001 Reference proteome <br />
4 b0001 Threonine biosynthesis <br />
5 b0002 3D-structure <br />
6 b0002 ATP-binding <br />
7 b0002 Allosteric enzyme <br />
8 b0002 Amino-acid biosynthesis <br />
9 b0002 Direct protein sequencing<br />
10 b0002 Kinase <br />
# … with 27,298 more rows<br />
</pre><br />
<br />
Maintenant, il ne s'agit plus que de regrouper les ''bnumbers'' par mot-clé :<br />
<source lang='rsplus'><br />
ref_sets = keywords %>% <br />
group_by(keyword) %>%<br />
summarise(count=n(), elements = list(bnumber)) %>%<br />
ungroup %>%<br />
filter(count>1) %>%<br />
select(set.id=keyword, set.desc=count, elements)<br />
ref_sets<br />
</source><br />
<pre><br />
# A tibble: 333 x 3<br />
set.id set.desc elements <br />
<chr> <int> <list> <br />
1 2Fe-2S 24 <chr [24]> <br />
2 3D-structure 1571 <chr [1,571]><br />
3 3Fe-4S 7 <chr [7]> <br />
4 4Fe-4S 112 <chr [112]> <br />
5 Acetylation 100 <chr [100]> <br />
6 Activator 116 <chr [116]> <br />
7 Acyltransferase 68 <chr [68]> <br />
8 ADP-ribosylation 4 <chr [4]> <br />
9 Allosteric enzyme 38 <chr [38]> <br />
10 Alternative initiation 7 <chr [7]> <br />
# … with 323 more rows<br />
</pre><br />
<br />
Pour utiliser "facilement" ces données avec python, nous allons sauvegarder le tibble au format JSON :<br />
<source lang='rsplus'><br />
library(jsonlite)<br />
ref_sets %>% toJSON %>% write("reference.sets/uniprot.keywords.sets.json")<br />
</source><br />
<br />
==== Script de recherche d'enrichissement ====<br />
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python script<br />
<br />
Ecocyc<br />
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=== Base de données ===<br />
<br />
<br />
== Approche par matrice ou graphe non orienté ==</div>
Barriot