Construction et Analyse de R´ eseaux de G` enes Contextuels dans le Domaine V´ eg´ etal
Marc Legeay 1,2 B´eatrice Duval 1 Jean-Pierre Renou 2 Julie Bourbeillon 2
1 LERIA - Universit´e d’Angers - UNAM,
2 boulevard Lavoisier, 49045 Angers, Cedex 01, France
2 INSTITUT DE RECHERCHE EN HORTICULTURE ET SEMENCES (IRHS), UMR1345 INRA-Universit´e d’Angers-AgroCampus Ouest, Centre Angers-Nantes,
42 rue Georges Morel - BP 60057, 49071, Beaucouz´e, Cedex, France
Probl´ematique
Un des probl`emes actuels en bioinformatique est de comprendre les m´ecanismes de r´egulation au sein d’une cellule. Notre travail concerne l’´etude des r´eseaux de g`enes, avec la particularit´e d’y int´egrer les acteurs encore mal connus que sont les ARN anti-sens. Plusieurs ´ etudes pointent l’importance de la r´egulation par les anti-sens dans les ph´enom`enes de r´eponses aux stress. Pour ´etudier l’impact des anti-sens dans les r´eseaux de g`enes, nous ´etudions leur comportement dans deux contextes exp´erimentaux d’un processus biologique de stress.
Donn´ees
Nous travaillons sur des donn´ees transcriptomiques issues de pommiers, grˆ ace ` a la puce ` a ADN AryANE version 1. La puce est constitu´ee de 126 022 sondes, avec autant de sondes sens que de sondes anti-sens. Nous ´etudions le processus de la maturation du fruit d´ecrit par deux conditions : la r´ecolte (H), et 60 jours apr`es la r´ecolte (60DAH).
Chaque condition est form´ee de 22 ´echantillons de fruit, ` a chaque ´echantillon de H correspond un ´echantillon de 60DAH.
M´ethodologie
sense anti-sense sense anti-sense
Condition 1 Condition 2
genes of interest
Coexpression network Coexpression network
Module detection
Module network analysis
Module detection Functional informations
Motif detection
Module detection
Sense ontology Sense and anti-sense ontology
Specifics terms
Terms p-values
response to cold 5.6059e-05
... ...
Figure 1: Sch´ema de la m´ethodologie.
On dispose de donn´ees d’expression de g`enes sens et anti-sens dans deux conditions illustrant la r´eponse ` a un stress.
1 Recherche des g`enes d’int´erˆet ;
2 Identification des fonctions biologiques associ´ees aux g`enes d’int´ erˆet sens et sens/anti-sens ;
3 Calcul des termes sp´ecifiques ` a l’ensemble sens/anti-sens ;
4 Construction contextuelle des r´eseaux pour les g`enes d’int´erˆet ;
5 D´etection des modules dans chacun des r´eseaux ;
6 Analyse des r´eseaux via les modules et les termes sp´ecifiques.
G`enes d’int´erˆet
Un g` enes sens ou anti-sens est un g`ene d’int´erˆet si la diff´erence du niveau d’expression entre les deux conditions exc`ede 1 log.
Figure 2: Profils d’expression de deux g`enes d’int´erˆet.
S AS
e(g AS )=0 (731)
e(g S )=e(g AS ) (196)
e(g S )=0 (494)
e(g S )≠e(g AS ) (4) e(g S )≠0
(931)
e(g AS )≠0 (694)
Figure 3: R´epartition des g`enes d’int´erˆet.
Etude fonctionnelle ´
response to heat
response to osmotic stress response to salt stress
response to wounding response to temperature stimulus
hyperosmotic response response to cold response to disaccharide
response to cadmium ion
response to hydrogen peroxide response to metal ion response to sucrose
response to reactive oxygen species
response to karrikin response to desiccation response to oxygen levels
response to decreased oxygen levels
response to topologically incorrect protein
response to misfolded protein response to water
response to water deprivation response to oxidative stress response to cytokinin
gibberellic acid mediated signaling pathway
defense response to bacterium defense response to other organism
defense response
systemic acquired resistance systemic acquired resistance, salicylic acid mediated signaling pathway response to endoplasmic reticulum
stress
defense response, incompatible interaction response to abscisic acid
response to brassinosteroid response to carbohydrate
response to inorganic substance
response to gibberellin response to alcohol
response to organic cyclic compound
jasmonic acid mediated signaling pathway gibberellin mediated signaling
pathway cellular response to gibberellin
stimulus response to salicylic acid
cellular response to salicylic acid stimulus
response to abiotic stimulus
response to stress cellular response to jasmonic acid
stimulus response to jasmonic acid cellular response to organic cyclic
compound response to hormone response to acid chemical
response to oxygen-containing compound response to lipid response to nitrate
response to organic substance
pigment accumulation in response to UV light anthocyanin accumulation in tissues in response to UV light long-day photoperiodism ion transmembrane transport
ammonium transmembrane transport
pigment accumulation drug transmembrane transport
drug transport photoperiodism
pigment accumulation in tissues in response to UV light
diterpenoid catabolic process terpenoid metabolic process
lipid oxidation cell death pigmentation
signaling
isoprenoid metabolic process
fatty acid catabolic process fatty acid metabolic process
regulation of biological quality monocarboxylic acid metabolic
process single-organism cellular process regulation of hormone levels
gibberellin catabolic process biological_process
monocarboxylic acid catabolic process
lipid modification inorganic cation transmembrane
transport
inorganic ion transmembrane transport amide transport
urea transport
urea transmembrane transport amine transport organic acid transport
organic acid transmembrane transport
ion transport
single-organism localization photoperiodism, flowering
localization transmembrane transport
pigment accumulation in tissues long-day photoperiodism, flowering
fatty acid oxidation programmed cell death
very long-chain fatty acid metabolic process
fatty acid beta-oxidation multi-organism process
cell communication immune system process
terpenoid catabolic process
xenobiotic metabolic process single organism signaling
isoprenoid catabolic process single-organism process
diterpenoid metabolic process circadian rhythm
death
multicellular organismal process rhythmic process
cell surface receptor signaling pathway cellular response to xenobiotic
stimulus
cellular response to stimulus
response to other organismsalicylic acid mediated signaling pathway innate immune response immune response hormone-mediated signaling
pathway
signal transduction intracellular signal transduction
response to fungus response to bacterium second-messenger-mediated
signaling
MAPK cascade response to external stimulus
transmembrane receptor protein tyrosine kinase signaling pathway
response to xenobiotic stimulus
host programmed cell death induced by symbiont response to UV
response to drug
cellular response to stress plant-type hypersensitive response
response to biotic stimulus detection of biotic stimulus response to external biotic stimulus
response to stimulus
enzyme linked receptor protein signaling pathway
cellular response to chemical stimulus
response to high light intensity nonphotochemical quenching response to far red light response to red light
response to red or far red light
energy quenching response to light intensity response to blue light
response to light stimulus response to UV-B
detection of stimulus cellular response to acid chemical
cellular response to oxygen-containing compound response to endogenous stimulus
cellular response to organic substance cellular response to endogenous
stimulus response to chemical
cellular response to lipid
cellular response to hormone stimulus response to nitrogen compound
response to radiation calcium ion transport
L-amino acid transport L-arginine import
arginine import
transition metal ion transport L-amino acid import
amino acid import L-arginine transport
dicarboxylic acid transport
arginine transport
divalent inorganic cation transport dipeptide transport
neutral amino acid transport
oligopeptide transport
basic amino acid transport
metal ion transport proline transport amino acid transport
divalent metal ion transport
cation transport
cation transmembrane transport ammonium transport
monovalent inorganic cation transport
anion transmembrane transport organic substance transport
glycerol transport
organic anion transport carboxylic acid transport myo-inositol transport
peptide transport
polyol transport nectar secretion
nitrogen compound transportanion transport inorganic anion transport
nitrate transport
organic cation transport
methylammonium transport
intracellular transport
protein targeting
establishment of protein localization
single-organism transport single-organism intracellular
transport intracellular protein transport
protein localization protein transportfluid transport
one-carbon compound transport carbohydrate transport
secretion water transport
transport organic hydroxy compound
transport
cation homeostasis
vegetative to reproductive phase transition of meristem
single-organism cellular localization protein localization to membrane seedling developmentcellular ion homeostasis
macromolecule localization cellular protein localization
establishment of localization establishment of protein
localization to membrane
cellular localization establishment of localization in cell
cellular cation homeostasis cellular macromolecule localization protein targeting to membrane
root epidermal cell differentiation
plant epidermal cell differentiation root hair cell development plant epidermis development
trichoblast differentiation
trichoblast maturation root hair cell differentiation
anatomical structure morphogenesis
cellular developmental processmultidimensional cell growth single-organism developmental
process
developmental cell growth developmental growth
developmental process meristem development root development
root morphogenesis developmental maturation
aging anatomical structure development anatomical structure maturation
organ development root system development
tissue development androecium development phyllome development
cell growth gibberellin metabolic process
carboxylic acid metabolic process cellular component morphogenesis
organelle organization unidimensional cell growth
membrane organization
plastid organization monocarboxylic acid biosynthetic
process cellular chemical homeostasis
reproductive process
homeostatic process single-organism membrane
organization cellular homeostasis chemical homeostasis
meristem maintenance
growth single-multicellular organism
process fruit development
shoot system development system development post-embryonic organ development reproductive system development
flower development
stamen development
fruit ripening
cell maturation cell differentiationcell development
root hair elongation developmental growth involved in
morphogenesis
cell morphogenesis floral whorl development
anther development floral organ development
post-embryonic development
single organism reproductive process reproductive structure development
developmental process involved in reproduction reproductive shoot system
development ion homeostasis
multicellular organismal development
cellular modified amino acid biosynthetic process
heterocycle metabolic process
organic cyclic compound catabolic process heterocycle catabolic process organonitrogen compound
metabolic process
cellular nitrogen compound metabolic process carbohydrate biosynthetic process
cellular macromolecule catabolic process purine nucleoside metabolic
process carbohydrate catabolic process carbohydrate metabolic process
macromolecule biosynthetic process
purine ribonucleoside metabolic process
pyridine-containing compound metabolic process purine-containing compound
metabolic process nucleobase-containing compound
metabolic process
allantoin catabolic process sulfur compound metabolic process
aromatic amino acid family metabolic process
reductive pentose-phosphate cycle generation of precursor metabolites and energy
allantoin metabolic process catabolic process
cellular modified amino acid metabolic process nitrogen compound metabolic
process glycosyl compound biosynthetic
process cellular aromatic compound
metabolic process
organonitrogen compound catabolic process amine metabolic process heterocycle biosynthetic process
cytokinin metabolic process photosynthesis
photosynthesis, dark reaction cell wall organization or biogenesis
single-organism carbohydrate catabolic process organic substance metabolic
process cellular catabolic process cellular metabolic process
carbohydrate derivative biosynthetic process
glycosyl compound metabolic process
organic cyclic compound metabolic process primary metabolic process
organic substance biosynthetic process
single-organism carbohydrate metabolic process
organic substance catabolic process thioester metabolic process nucleoside metabolic process
flavonoid metabolic processorganophosphate biosynthetic process steroid biosynthetic process
protein phosphorylation inositol phosphate metabolic
process flavonoid biosynthetic process
sterol metabolic process
steroid metabolic process alcohol biosynthetic process
biological regulation alcohol metabolic process
coenzyme metabolic process glycoprotein catabolic process
nucleotide metabolic process
oxidoreduction coenzyme metabolic process macromolecule modification protein metabolic process carbohydrate derivative catabolic process
macromolecule catabolic process
cellular protein metabolic process ribonucleoside metabolic processnicotinamide nucleotide metabolic
process glycoprotein metabolic process
pyridine nucleotide metabolic process
purine ribonucleotide metabolic process cofactor metabolic process
ribose phosphate metabolic process phosphate-containing compound
metabolic process organophosphate metabolic
process glyceraldehyde-3-phosphate
metabolic process glucose 6-phosphate metabolic
process nucleoside phosphate metabolic
process purine ribonucleoside monophosphate metabolic process pyruvate metabolic process
organic hydroxy compound metabolic process lipid biosynthetic process small molecule biosynthetic process
cellular lipid catabolic process small molecule metabolic process organic hydroxy compound
biosynthetic process
polyol metabolic process regulation of meristem growth
anthocyanin-containing compound metabolic process pigment metabolic process phytosteroid biosynthetic process
anthocyanin-containing compound biosynthetic process
phytosteroid metabolic process brassinosteroid metabolic process
brassinosteroid biosynthetic process signal transduction by protein
phosphorylation
ribonucleotide metabolic process
NADP metabolic process acyl-CoA metabolic processcellular protein modification
process
acetyl-CoA metabolic process pentose-phosphate shunt
protein modification process protein catabolic process phosphorus metabolic process carbohydrate derivative metabolic
process glycolytic process lipid catabolic process nucleobase-containing small molecule metabolic process cytokinin catabolic process
lignin biosynthetic process
sulfur amino acid metabolic process cellular amino acid biosynthetic
process
photosynthetic electron transport chain cellular metabolic compound
salvage
external encapsulating structure organization cellular amino acid catabolic
process cellular component organization Golgi organization
glucosinolate metabolic process endomembrane system
organization
alpha-amino acid biosynthetic process cysteine biosynthetic process serine family amino acid
biosynthetic process
macromolecular complex subunit organization glycine catabolic process
glycine metabolic process serine family amino acid catabolic
process serine family amino acid metabolic
process
glycine decarboxylation via glycine cleavage system
alpha-amino acid catabolic process
polyamine catabolic process proteasome core complex assembly
cellular biogenic amine catabolic process
cellular biogenic amine metabolic process proteasome assembly
photosynthesis, light harvesting in photosystem I photosynthetic electron transport
in photosystem I cellular component biogenesis photorespiration
glucosinolate biosynthetic process alpha-amino acid metabolic process cysteine metabolic process
amine catabolic process cellular component assembly
sulfur amino acid biosynthetic process
cellular macromolecular complex assembly
cellular protein complex assembly protein complex subunit organization macromolecular complex assembly
protein complex assembly
photosystem II assembly protein complex biogenesis
polyamine metabolic process cell wall modification
plant-type cell wall organization
gluconeogenesis hexose biosynthetic process
cell wall pectin metabolic process
plant-type cell wall loosening glucose metabolic process plant-type cell wall modification
photosynthesis, light harvesting
cell wall organization
plant-type cell wall organization or biogenesis photosynthesis, light reaction
cellular amine metabolic process ribonucleoprotein complex
biogenesis
phenylpropanoid biosynthetic process carboxylic acid biosynthetic process cellular component organization or
biogenesis oxoacid metabolic process
hormone metabolic process cellular process lignin metabolic process
secondary metabolic process oxidation-reduction process carboxylic acid catabolic process
electron transport chain
hormone catabolic processsecondary metabolite biosynthetic process glycosinolate metabolic process
phenylpropanoid metabolic process biosynthetic process organic acid biosynthetic process toxin metabolic process
secondary metabolite catabolic process
metabolic process organic acid metabolic process
organic cyclic compound biosynthetic process
organic acid catabolic process benzene-containing compound
metabolic process aromatic compound biosynthetic
process
pigment biosynthetic process single-organism metabolic process
salicylic acid metabolic process
lipid metabolic process hormone biosynthetic process
cellular aldehyde metabolic process salicylic acid biosynthetic process
small molecule catabolic process phenol-containing compound
biosynthetic process cellular lipid metabolic process
cellular hormone metabolic process glycosinolate biosynthetic process
coumarin biosynthetic process
cellular amino acid metabolic process
organonitrogen compound biosynthetic process
S-glycoside biosynthetic process coumarin metabolic process
cellular biosynthetic process sulfur compound biosynthetic
process
single-organism catabolic process phenol-containing compound
metabolic process toxin catabolic process S-glycoside metabolic process
carbon fixation single-organism biosynthetic
process
regulation of innate immune response
regulation of defense response regulation of plant-type hypersensitive response
regulation of phosphate metabolic process regulation of hydrogen peroxide metabolic process regulation of programmed cell
death
regulation of protein modification process negative regulation of protein
metabolic process
regulation of dephosphorylation regulation of proteolysis
regulation of protein dephosphorylation negative regulation of proteolysis
negative regulation of autophagy regulation of peptidase activity
negative regulation of peptidase activity
negative regulation of catabolic process positive regulation of biosynthetic
process
regulation of cellular catabolic process regulation of biosynthetic processregulation of macromolecule
metabolic process regulation of primary metabolic
process regulation of multicellular
organismal process
regulation of biological process regulation of cellular process
regulation of localization
regulation of immune system process
positive regulation of biological process
regulation of response to stimulus
negative regulation of cellular process negative regulation of biological
process
negative regulation of defense response
regulation of phosphorus metabolic process regulation of response to stress
regulation of proton transport
regulation of reactive oxygen species metabolic process regulation of photosynthesis regulation of ion transport
negative regulation of cellular catabolic process
regulation of autophagy regulation of protein metabolic
process regulation of flavonoid biosynthetic
process regulation of hydrolase activity
regulation of cellular protein metabolic process
positive regulation of flavonoid
biosynthetic process negative regulation of cellular
protein metabolic process negative regulation of hydrolase
activity
negative regulation of macromolecule metabolic process negative regulation of catalytic
activity positive regulation of catalytic
activity regulation of catalytic activity
regulation of catabolic process regulation of cellular metabolic
process negative regulation of metabolic
process positive regulation of metabolic
process regulation of metabolic process
negative regulation of cellular metabolic process regulation of multicellular
organismal development
regulation of developmental process myo-inositol hexakisphosphate
biosynthetic process
regulation of growth cholesterol metabolic process
cholesterol biosynthetic process
inositol phosphate biosynthetic process polyol biosynthetic process
phosphorylation regulation of developmental growth regulation of meristem
development sterol biosynthetic process
myo-inositol hexakisphosphate metabolic process
nucleoside monophosphate metabolic process
negative regulation of molecular function ribonucleoside monophosphate
metabolic process
positive regulation of molecular function regulation of molecular function
purine nucleoside monophosphate metabolic process
negative regulation of response to stimulus regulation of immune response regulation of cellular response to
stress regulation of cell death regulation of transport
pectin metabolic process
cellulose metabolic process beta-glucan metabolic process
galacturonan metabolic process plant-type cell wall cellulose
metabolic process rRNA processing
gene expression cellular polysaccharide metabolic
process RNA metabolic process ribosome biogenesis
cell wall polysaccharide metabolic process hexose metabolic process
ncRNA processing
starch metabolic process RNA processing
cellular glucan metabolic process
rRNA metabolic process glucan metabolic process
ncRNA metabolic process monosaccharide biosynthetic
process cellular amide catabolic process
monosaccharide metabolic process cellular amide metabolic process
cellular nitrogen compound catabolic process
cell wall macromolecule metabolic process polysaccharide biosynthetic process
macromolecule metabolic process cellular macromolecule metabolic
process cellular carbohydrate metabolic
process
polysaccharide metabolic process nucleic acid metabolic process
purine nucleotide metabolic process
(a) Ontologie des g`enes d’int´erˆet.
transition metal ion transport L-arginine transport
neutral amino acid transport
calcium ion transport arginine import
L-arginine import
fatty acid oxidation
fatty acid catabolic process lipid oxidation
fatty acid beta-oxidation
anthocyanin-containing compound biosynthetic process very long-chain fatty acid metabolic process
signal transduction by protein phosphorylation
detection of stimuluscellular response to salicylic acid stimulus
defense response to bacterium salicylic acid mediated signaling
pathway jasmonic acid mediated signaling
pathway cellular response to jasmonic acid
stimulus
enzyme linked receptor protein signaling pathway
response to endoplasmic reticulum stress transmembrane receptor protein
tyrosine kinase signaling pathway
defense response to other organism
response to hydrogen peroxide
response to water
response to topologically incorrect protein response to oxidative stress
response to heat response to cold response to water deprivation
response to oxygen levels nonphotochemical quenching
energy quenching response to high light intensity
drug transport
drug transmembrane transport monovalent inorganic cation
transport
cation transmembrane transport
photoperiodism
regulation of meristem development
regulation of developmental growth cholesterol metabolic process
regulation of developmental process regulation of multicellular organismal development protein phosphorylation
phosphorylation MAPK cascade
cholesterol biosynthetic process
positive regulation of metabolic process
negative regulation of defense response positive regulation of molecular
function
regulation of photosynthesis positive regulation of biological
process
negative regulation of response to stimulus acetyl-CoA metabolic process
regulation of response to stimulus
positive regulation of catalytic activity
negative regulation of hydrolase activity
negative regulation of catabolic process
regulation of phosphorus metabolic process
negative regulation of proteolysis regulation of peptidase activity
regulation of phosphate metabolic process
negative regulation of autophagy
negative regulation of peptidase activity
hyperosmotic response response to desiccation response to decreased oxygen
levels
response to misfolded protein
S-glycoside biosynthetic process secondary metabolite catabolic
process glycosinolate metabolic process
glycosinolate biosynthetic process
aromatic amino acid family metabolic process cellular biosynthetic process
growth meristem development
cell growth single-organism membrane
organization meristem maintenance anatomical structure maturation
cellular component morphogenesis cellular developmental process
membrane organization
plastid organization cell morphogenesis
glycine decarboxylation via glycine cleavage system
macromolecular complex subunit organization
photorespiration cellular metabolic compound
salvage
glucosinolate biosynthetic process glucosinolate metabolic process
dicarboxylic acid transport
single-organism intracellular transport myo-inositol transport
carbohydrate transport polyol transport
intracellular transport
reproductive system development
shoot system development
post-embryonic development vegetative to reproductive phase
transition of meristem
anther development developmental process involved in
reproduction reproductive structure development
fruit ripening
glucose metabolic process ribosome biogenesis
ncRNA processing hexose biosynthetic process
cellulose metabolic process hexose metabolic process
gluconeogenesis
toxin catabolic process phenol-containing compound
metabolic process photoperiodism, flowering
S-glycoside metabolic process salicylic acid metabolic process phenol-containing compound
biosynthetic process multicellular organismal process
rhythmic process
salicylic acid biosynthetic process organic acid transmembrane transport
circadian rhythm
monosaccharide biosynthetic process proteasome core complex assembly
monosaccharide metabolic process allantoin catabolic process proteasome assembly
