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Context-specific co-expression networks to explore the impact of anti-sense transcription
Marc Legeay, Béatrice Duval, Jean-Pierre Renou
To cite this version:
Marc Legeay, Béatrice Duval, Jean-Pierre Renou. Context-specific co-expression networks to explore the impact of anti-sense transcription. 13th conference on Computational Methods for Systems Biology (CMSB’15), Sep 2015, Nantes, France. 2015. �hal-02516452�
Context-specific co-expression networks to explore the impact of anti-sense transcription
Marc Legeay
1,2B´eatrice Duval
1Jean-Pierre Renou
21
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
Motivations
Understanding the regulation mechanisms in a cell is a key issue in bioinformatics. Anti-sense RNAs are endogenous RNA molecules whose partial or entire sequences exhibit complementarity to other transcripts. Their different functional roles are not completely known but some studies suggest that they play an important role in stress response mechanisms. A recent study with a full genome microarray for the apple has detected anti-sense transcription for 65% of expressed genes, which suggests a high potential of anti-sense regulation. Our work integrates anti-sense transcripts into context-specific gene networks and proposes a differential analysis of those networks.
Biological materials
We use microarray data of RNA extracted from the apple fruit (Malus × domestica) thanks to the chip AryANE v1.0 containing 63011 predicted sense genes and 63011 complementary anti-sense sequences. We study the fruit ripening process described by two conditions: harvest ( H ) and 60 days after harvest ( 60DAH ), and for each condition, 22 samples of apple fruit have been analyzed.
Methods
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
Revealed-by-AS terms
Terms p-values
response to cold 5.6059e-05
... ...
Figure 1: Diagram of the methods.
We start with expression data of sense and anti-sense genes in two stress-response conditions. From there, we propose five steps to analyse the role of anti-sense transcripts:
1
Identification of genes of interest: genes (sense and anti-sense) differentially expressed.
2
Functional analysis of genes of interest to com- pute the revealed-by-AS terms.
3
Contextual construction of gene network for the genes of interest. We construct a co-expression gene network for each condition from the expression of the genes of interest.
4
Module detection. In each network, we look for highly correlated genes by grouping them in mod- ules thanks to a hierarchical clustering .
5
Network analysis, this work is in progress.
Genes of interest
With a threshold of 1 log change between the two conditions, we found 931 sense (S ) and 694 anti-sense probes (AS ) differentially expressed, with among them, 200 genes (S ∪ AS ) for which both sense and anti-sense fulfill the condition.
Figure 2: Expression profile of two genes of interest.
S AS
e(gAS)=0 (731)
e(gS)=e(gAS) (196)
e(gS)=0 (494)
e(gS)≠e(gAS) (4) e(gS)≠0
(931)
e(gAS)≠0 (694)
Figure 3: Genes of interest distribution.
Functional analysis
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 organism salicylic 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
Figure 4: Ontology of all the genes of interest.
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
Figure 5: Revealed-by-AS terms.
In order to study the impact of anti-sense transcription, we compare the ontological terms significantly represented in the set S ∪ AS of sense and anti-sense genes (Figure 4) with the ontological terms significantly represented in the set S of sense genes. The difference enables to define the revealed-by-AS terms (Figure 5).
ANTISENS EVOLUTION SENS AT
MDP0000151721 -1 -1 MDP0000151721_r AT5G67590 MDP0000223905 -1 -1 MDP0000223905_r AT2G39730 MDP0000272802 -1 -1 MDP0000272802_r AT5G67590 MDP0000561026 -1 -1 MDP0000561026_r AT2G36830 MDP0000944409 -1 -1 MDP0000944409_r AT2G39730 MDP0000132480 -1 0 MDP0000132480_r AT2G27710 MDP0000134273 -1 0 MDP0000134273_r AT2G26250 MDP0000134685 -1 0 MDP0000134685_r AT4G37930 MDP0000146698 -1 0 MDP0000146698_r AT5G38480 MDP0000151190 -1 0 MDP0000151190_r AT3G24120 MDP0000169619 -1 0 MDP0000169619_r AT1G56070 MDP0000206093 -1 0 MDP0000206093_r AT4G04330 MDP0000206314 -1 0 MDP0000206314_r AT3G05890 MDP0000215630 -1 0 MDP0000215630_r AT3G51780 MDP0000224974 -1 0 MDP0000224974_r AT3G61580 MDP0000231051 -1 0 MDP0000231051_r AT2G46210 MDP0000234570 -1 0 MDP0000234570_r AT4G37930 MDP0000237499 -1 0 MDP0000237499_r AT3G23050 MDP0000268045 -1 0 MDP0000268045_r AT1G15950 MDP0000297425 -1 0 MDP0000297425_r AT4G03280 MDP0000324254 -1 0 MDP0000324254_r AT4G24960 MDP0000325574 -1 0 MDP0000325574_r AT3G62410 MDP0000325582 -1 0 MDP0000325582_r AT3G62410 MDP0000564897 -1 0 MDP0000564897_r AT2G22430 MDP0000642609 -1 0 MDP0000642609_r AT3G53990 MDP0000760376 -1 0 MDP0000760376_r AT2G46210 MDP0000777793 -1 0 MDP0000777793_r AT1G56070 MDP0000797759 -1 0 MDP0000797759_r AT2G21660 MDP0000920069 -1 0 MDP0000920069_r AT1G64060 MDP0000310152 -1 1 MDP0000310152_r AT5G65730 MDP0000126738 0 -1 MDP0000126738_r AT3G18990 MDP0000132477 0 -1 MDP0000132477_r AT4G37930 MDP0000148186 0 -1 MDP0000148186_r AT1G32060 MDP0000241245 0 -1 MDP0000241245_r AT1G49480 MDP0000244771 0 -1 MDP0000244771_r AT3G55800 MDP0000287992 0 -1 MDP0000287992_r AT1G01060 MDP0000300321 0 -1 MDP0000300321_r AT3G45140 MDP0000317816 0 -1 MDP0000317816_r AT5G01600 MDP0000321244 0 -1 MDP0000321244_r AT2G39730 MDP0000429215 0 -1 MDP0000429215_r AT2G46590 MDP0000647652 0 -1 MDP0000647652_r AT4G17090 MDP0000835914 0 -1 MDP0000835914_r AT1G42970 MDP0000122458 0 1 MDP0000122458_r AT4G25140 MDP0000205588 0 1 MDP0000205588_r AT3G11170 MDP0000210504 0 1 MDP0000210504_r AT3G01570 MDP0000253300 0 1 MDP0000253300_r AT2G38560 MDP0000302532 0 1 MDP0000302532_r AT3G18990 MDP0000671114 0 1 MDP0000671114_r AT5G54770 MDP0000813339 0 1 MDP0000813339_r AT4G34710 MDP0000151030 1 0 MDP0000151030_r AT4G25140 MDP0000191203 1 0 MDP0000191203_r AT3G16785 MDP0000253809 1 0 MDP0000253809_r AT5G65020 MDP0000281110 1 0 MDP0000281110_r AT1G22770 MDP0000728753 1 0 MDP0000728753_r AT5G06860 MDP0000766240 1 0 MDP0000766240_r AT4G01370 MDP0000836165 1 1 MDP0000836165_r AT4G02330
Figure 6: Evolution of probes associated with the term ”response to cold”.
