Uptake and function of anthrax toxins

Oxidative Stress Induced Senescence

Bladder Cancer

SIDS Susceptibility Pathways

Regulation of toll-like receptor signaling pathway

Spinal Cord Injury

TSLP Signaling Pathway

Senescence and Autophagy in Cancer

Corticotropin-releasing hormone

Copper homeostasis

Hepatitis C and Hepatocellular Carcinoma

ERK Pathway in Huntington's Disease

Oxidative Damage

Prion disease pathway

TP53 Regulates Transcription of Cell Cycle Genes

DNA Damage Response

Gastric cancer network 2

DNA Damage Response (only ATM dependent)

Retinoblastoma Gene in Cancer

Ectoderm Differentiation

Aryl Hydrocarbon Receptor

Thyroid Stimulating Hormone (TSH) signaling pathway

TP53 Network

Integrated Cancer pathway

PPAR Alpha Pathway

Metastatic brain tumor

Integrated Breast Cancer Pathway

Neural Crest Differentiation

Caspase activation via Dependence Receptors in the absence of ligand

Mismatch Repair

Activation of anterior HOX genes in hindbrain development during early embryogenesis

Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation

MAPK Signaling Pathway

VEGFA-VEGFR2 Signaling Pathway

Branched-chain amino acid catabolism

Caspase activation via Death Receptors in the presence of ligand

Class I MHC mediated antigen processing & presentation

Glyoxylate metabolism and glycine degradation

Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism

Angiogenesis

NRF2 pathway

Focal Adhesion

PDGF Pathway

Differentiation Pathway

DNA Double Strand Break Response

DNA Damage/Telomere Stress Induced Senescence

Regulation of TP53 Activity through Phosphorylation

Wnt Signaling Pathway

IL-6 signaling pathway

TGF-beta Signaling Pathway

Nonhomologous End-Joining (NHEJ)

RAF-independent MAPK1/3 activation

Interleukin-20 family signaling

Resolution of Abasic Sites (AP sites)

Renin - Angiotensin System

HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)

SUMOylation of DNA replication proteins

DNA IR-Double Strand Breaks (DSBs) and cellular response via ATM

Apoptosis Modulation and Signaling

AMPK Signaling

ATM Signaling Pathway

Amyotrophic lateral sclerosis (ALS)

Signaling Pathways in Glioblastoma

Fluoropyrimidine Activity

Oncostatin M Signaling Pathway

TP53 Regulates Transcription of DNA Repair Genes

PRC2 methylates histones and DNA

TP53 Regulates Metabolic Genes

Melatonin metabolism and effects

Composition of Lipid Particles

Retinoid metabolism and transport

Nicotine Metabolism

Tamoxifen metabolism

Catalytic cycle of mammalian FMOs

Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3

SUMOylation of DNA damage response and repair proteins

Cellular response to heat stress

tRNA processing in the nucleus

Gene Silencing by RNA

SUMOylation of RNA binding proteins

SUMOylation of chromatin organization proteins

Signaling of Hepatocyte Growth Factor Receptor

Angiopoietin Like Protein 8 Regulatory Pathway

IL-4 Signaling Pathway

Phytochemical activity on NRF2 transcriptional activation

IL1 and megakaryotyces in obesity

Vitamin B12 Metabolism

Aryl Hydrocarbon Receptor Pathway

Selenium Micronutrient Network

Signaling by FGFR2

Signaling by FGFR4

Regulation of TP53 Activity through Association with Co-factors

Biochemical Pathways Part I

AtMetExpress overview

Amino Acid metabolism

Regulated Necrosis

Signaling by FGFR1

RHO GTPases Activate Formins

Major pathway of rRNA processing in the nucleolus and cytosol

Cardiac Progenitor Differentiation

Cardiac Hypertrophic Response

Cell Differentiation - Index

Toll Like Receptor 3 (TLR3) Cascade

RHO GTPases activate CIT

Mitochondrial biogenesis

MAPK6/MAPK4 signaling

Hedgehog 'on' state

Hedgehog 'off' state

TCF dependent signaling in response to WNT

C-type lectin receptors (CLRs)

TNFR2 non-canonical NF-kB pathway

Hedgehog ligand biogenesis

NIK-->noncanonical NF-kB signaling

Metabolism of polyamines

Beta-catenin independent WNT signaling

MECP2 and Associated Rett Syndrome

Prader-Willi and Angelman Syndrome

RANKL/RANK Signaling Pathway

Interleukin-11 Signaling Pathway

Serotonin Transporter Activity

NAD Biosynthesis II (from tryptophan)

NAD+ metabolism

NAD+ biosynthetic pathways

tRNA modification in the nucleus and cytosol

TP53 Regulates Transcription of Cell Death Genes

POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation

Lung fibrosis

ESC Pluripotency Pathways

Focal Adhesion-PI3K-Akt-mTOR-signaling pathway

Circadian rythm related genes

Regulation of TP53 Activity through Acetylation

Metallothioneins bind metals

FTO Obesity Variant Mechanism

Transcription factor regulation in adipogenesis

Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling

Metabolism of folate and pterines

Hematopoietic Stem Cell Differentiation

EPH-Ephrin signaling

RHO GTPases activate PAKs

FasL/ CD95L signaling

One carbon donor

Dopamine metabolism

Influenza A virus infection

Sulfation Biotransformation Reaction

AGE/RAGE pathway

Osteopontin Signaling

TWEAK Signaling Pathway

Arrhythmogenic Right Ventricular Cardiomyopathy

Iron uptake and transport

Myometrial Relaxation and Contraction Pathways

Regulation of TP53 Expression and Degradation

RHO GTPases Activate NADPH Oxidases

Endosomal Sorting Complex Required For Transport (ESCRT)

BDNF signaling pathway

Structural Pathway of Interleukin 1 (IL-1)

Nanoparticle-mediated activation of receptor signaling

IL-1 signaling pathway

RHO GTPases Activate Rhotekin and Rhophilins

SREBP signalling

Synaptic Vesicle Pathway

Amino acid synthesis and interconversion (transamination)

Sulfur amino acid metabolism

Base-Excision Repair, AP Site Formation

HDR through MMEJ (alt-NHEJ)

Fanconi Anemia Pathway

Regulation of Microtubule Cytoskeleton

Arylhydrocarbon receptor (AhR) signaling pathway

Gene regulatory network modelling somitogenesis

RHO GTPases activate IQGAPs

RHO GTPases activate KTN1

RHO GTPases activate PKNs

RHO GTPases Activate WASPs and WAVEs

Semaphorin interactions

RHO GTPases regulate CFTR trafficking

TNF signaling

Prostaglandin Synthesis and Regulation

Type II diabetes mellitus

Physiological and Pathological Hypertrophy of the Heart

Vitamin D Metabolism

Nicotine Activity on Dopaminergic Neurons

Endothelin Pathways

Nicotine Activity on Chromaffin Cells

Calcium Regulation in the Cardiac Cell

T-Cell Receptor and Co-stimulatory Signaling

MFAP5-mediated ovarian cancer cell motility and invasiveness

G Protein Signaling Pathways

Wnt Signaling in Kidney Disease

T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection

Cannabinoid receptor signaling

Angiotensin II signaling (acute) in thick ascending limbs

Signaling by Leptin

Oncogene Induced Senescence

Signaling by FGFR3

Glycerophospholipid Biosynthetic Pathway

Leptin Insulin Overlap

Regulation of TP53 Activity through Methylation

Apoptosis-related network due to altered Notch3 in ovarian cancer

Quercetin and Nf-kB/ AP-1 Induced Cell Apoptosis

IL17 signaling pathway

TFs Regulate miRNAs related to cardiac hypertrophy

Leptin signaling pathway

Zinc homeostasis

tRNA processing in the mitochondrion

BDNF-TrkB Signaling

B-WICH complex positively regulates rRNA expression

DNA methylation

Farnesoid X Receptor Pathway

Amine-derived hormones

tRNA modification in the mitochondrion

ATR Signaling

mTOR signalling

Regulation of beta-cell development

Interferon type I signaling pathways

POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation

Lipid Droplet Metabolism

Lipid Metabolism Pathway

Effect of L-carnitine on metabolism

Serotonin and anxiety-related events

Serotonin and anxiety

SIRT1 negatively regulates rRNA expression

NoRC negatively regulates rRNA expression

SUMOylation of transcription factors

Primary Focal Segmental Glomerulosclerosis FSGS

ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression

Heart Development

Mitochondrial Gene Expression

Differentiation of white and brown adipocyte

Cori Cycle

Glycogen Metabolism

Glucuronidation

TCA Cycle Nutrient Utilization and Invasiveness of Ovarian Cancer

Genetic Interactions Between Sugar and Hormone Signaling

Glucouse Sensing and Signaling in Arabidopsis

Fructose Metabolism in Proximal Tubules

Hexoses metabolism in proximal tubules

Monoamine Transport

Mitochondrial translation

BMAL1:CLOCK,NPAS2 activates circadian gene expression

Selenoamino acid metabolism

Cardiac conduction

Endoderm Differentiation

G alpha (z) signalling events

DNA IR-damage and cellular response via ATR

Transcriptional Regulation by E2F6

ESR-mediated signaling

Signaling by PTK6

Purine metabolism

Pyrimidine metabolism and related diseases

SUMOylation of intracellular receptors

Peroxisomal protein import

DNA Replication Pre-Initiation

SUMOylation of transcription cofactors

Transcriptional regulation by RUNX2

Class B/2 (Secretin family receptors)

COPI-mediated anterograde transport

Cellular hexose transport

Interleukin-15 signaling

p75 NTR receptor-mediated signalling

Class A/1 (Rhodopsin-like receptors)

OAS antiviral response

Signaling by Erythropoietin

Interleukin-9 signaling

Regulation of RUNX2 expression and activity

SUMOylation of DNA methylation proteins

SUMOylation of immune response proteins

Transcriptional Regulation by MECP2

Integrin alphaIIb beta3 signaling

Signaling by NTRK2 (TRKB)

Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation

G-protein beta:gamma signalling

Signaling by Retinoic Acid

NO/cGMP/PKG mediated Neuroprotection

Fibrin Complement Receptor 3 Signaling Pathway

Viral Acute Myocarditis

miRNAs involvement in the immune response in sepsis

Non-genomic actions of 1,25 dihydroxyvitamin D3

SUMOylation of ubiquitinylation proteins

SUMOylation of SUMOylation proteins

Glutamate binding, activation of AMPA receptors and synaptic plasticity

Disorders of the Krebs cycle

G alpha (q) signalling events

Breast cancer pathway

G alpha (i) signalling events

Signaling by NTRK3 (TRKC)

Activation of NMDA receptors and postsynaptic events

Biosynthesis of DHA-derived SPMs

Biosynthesis of EPA-derived SPMs

Biosynthesis of electrophilic ?-3 PUFA oxo-derivatives

Biosynthesis of DPA-derived SPMs

PI3K Cascade

Nonalcoholic fatty liver disease

Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways

Metapathway biotransformation Phase I and II

Estrogen signaling pathway

Serotonin Receptor 4/6/7 and NR3C Signaling

Toll-like Receptor Signaling Pathway

The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeast’s industrial value is still urgently needed. Here, we analyzed 5400 growth curves obtained from 36 S. cerevisiae strains and comprehensively profiled their resistances against 13 industrially relevant stresses. We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions, however, plant isolates tend to have wider range of resistance, which may be associated with their metabolome and fluxome signatures in TCA cycle and fatty acid metabolism. By deep genomic sequencing we found that industrial strains have more genomic duplications especially affecting transcription factors, presenting disparate evolutionary paths in comparison to the environmental strains which have more InDels, gene deletions and strain-specific genes. Genome-wide association studies coupled with protein-protein interaction networks uncovered novel genetic determinants of stress resistances. These resistance-related engineering targets and strain rankings provide a valuable source for engineering significantly improved industrial platform strains.
This metabolomic study of 36 yeast strains measured intra- and extracellular metabolome under standard glucose medium, profiled by GS-MS. This is part of a multi-omic study on yeast strain collection.

Linking genetic, metabolic and phenotypic diversity 1 among S. cerevisiae strains using multi-omics associations

A FAIR principle describes an essential aspects of FAIR.
FAIR Principle

Accessible

the protocol is open, free, and universally implementable

the protocol allows for an authentication and authorization procedure, where necessary

Interoperable

(meta)data use vocabularies that follow FAIR principles

(meta)data include qualified references to other (meta)data

Reusable

(meta)data meet domain-relevant community standards

Nanopublications representing the FAIR Principles

Homo sapiens

maltose

Recon 2.2: from reconstruction to model of human metabolism

glycochenodeoxycholate (1-)

N-benzoylglycinate (1-)

Nelumbo nucifera

geranylacetone

Comparative analysis of essential oil components and antioxidant activity of extracts of Nelumbo nucifera from various areas of China.

N-acetyl-D-glucosamine (complete stereochemistry)

Cataglyphis diehlii

(2S)-2-Methyl-1-hexanol

(S)-2-Methyl-1-hexanol, characteristic mandibular gland substance of ants of the Cataglyphis bicolor group

Cataglyphis isis

Cataglyphis nodus

Ascophyllum nodosum

Tetrafucol A

Effects of phlorotannins from Ascophyllum nodosum (brown seaweed) on in vitro ruminal digestion of mixed forage or barley grain

Tetraphlorethol C

myristoleic acid

Nanopublications based on statements in Wikidata that specify in which species a particular molecule acts as metabolite, including reference on which that statement is based.
Wikidata Metabolite-Species Nanopublications, version 20190114_2136

Wikidata Metabolite-Species Nanopublications, version 20190217_1246

ethanol

[Formylmethyl]Trimethyl-Ammonium, N,N,N-Trimethylammonium Acetaldehyde

hordenine

lipoamide

Nicotinamide adenine dinucleotide

folic acid

riboflavin

niacin

calcitriol

calcifediol

7-dehydrocholesterol

ALDH2

ensembl Release 94

perillyl alcohol

harman

leucodopachrome

γ-tocopherol

citric acid

WikiPathways

formaldehyde

maltose (2 ring structure, stereospecific)

hydrogen peroxide

hydroxyprogesterone

cytosine

naphthalene

pantothenic acid

acetylcholine

uracil

L-Serine

L-Cysteine

L-Threonine

adenosine

PGG2

acetol

pristanic acid

taurine

levocarnitine

γ-aminobutyric acid

4-oxo-nonenal

Acetoacetate

O-toluric acid

oxitriptan

D-glucose (closed ring structure, complete stereochemistry)

4a-hydroxytetrahydrobiopterin

sedoheptulose 7-phosphate(2-)

thyrotropin-releasing hormone

nocodazole

D-erythrose 4-phosphate(2-)

Thymidine diphosphate glucose

N(2)-acetyl-L-ornithine

4'-hydroxydiclofenac

sn-glycerol 3-phosphate(2-)

Escherichia coli

o-tolualdehyde

Solanum lycopersicum

(-)-methyl jasmonate

Induced defences in plants reduce herbivory by increasing cannibalism

reducednicotinamide-adenine dinucleotide phosphate

zinc(2+)

L-homocysteine

DL-serine

CDP-ethanolamine

tamoxifen N-beta-D-glucosiduronic acid

Phomin

(E)-endoxifen

Prostacyclin (not favourable)

5-methyltetrahydrofolate(2-)

3-(6-methylpyridin-2-yl)-N-phenyl-4-quinolin-4-ylpyrazole-1-carbothioamide

FADH2 (2-)

6-Sulphatoxymelatonin

GT3

(+/-)-Colchicine

alpha-Hydroxy-N-desmethyltamoxifen

Plicamycin

(S)-sulindac

docosanoyl-CoA

Bleomycin

GQ1c

aflatoxin Q1

17beta-estradiol 17-glucosiduronic acid

aflatoxin m1

2-(N-Hydroxy-2,6-dichloroanilino)-5-hydroxybenzeneacetic acid

Benzo[a]pyrene-1,6-dione

IP3

4-Methoxyestrone

2-monoacylglycerol

O-phospho-L-serine

16α-hydroxyestrone

20α-hydroxycholesterol

11-cis-retinol

(R)-12-hpete

20-hydroxy-LTB4

25-hydroxycholesterol

2'-deoxyinosine

2-methyl-3-oxopropanoate

4-oxobutanoate

5,6-epoxyeicosatrienoic acid

cholesteryl sulfate

D-Alanine

dimethylallyl diphosphate

D-xylose (open structure, complete stereochemistry)

hexadecanal

LXA4

(+/-)-noradrenaline

trigonellamide

Nω-hydroxyarginine

oxalate

phosphoethanolamine

(R)-5-diphosphomevalonic acid

(S)-3-amino-2-methylpropanoate

sphinganine 1-phosphate

trans-4-hydroxyproline

trans-(-)-carveol

2-hydroxyphytanoyl-CoA

3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oyl-CoA

N-acetylmethionine

D-glyceraldehyde

L-Iso-Aspartate

2-Amino-3-Ketobutyric Acid

(S)-propylene glycol

S-sulfocysteine

Diureido-Acetate

maltotetraose

2-hydroxyestradiol

pentanoyl-CoA

3-O-beta-D-galactosyl-sn-glycerol

aquacob(III)alamin

isocitrate(3-)

3-(4-deoxy-beta-D-gluc-4-enosyluronic acid)-N-acetyl-D-glucosamine

homogentisate

5alpha-cholesta-7,24-dien-3beta-ol

(R)-3-aminoisobutyric acid

oxaloacetate(2-)

3-hydroxypropionate

3alpha,7alpha-dihydroxy-5beta-cholestan-26-oic acid

D-glycerate

4-methylthio-2-oxobutanoate

5,6-dihydroxyindole-2-carboxylate

N-acetyl-L-aspartate(2-)

1-piperideine-6-carboxylate

hexanoate

aldehydo-N-acetyl-D-mannosamine

taurolithocholate

3-hydroxy-L-kynurenine

psychosine sulfate

6-amino-2-oxohexanoic acid

S(8)-(2-methylpropanoyl)dihydrolipoamide

26-hydroxycholesterol

4,4-dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol

4-hydroxybenzoate

keto-phenylpyruvate

4-fumarylacetoacetate(2-)

3-phosphonatooxypyruvate(3-)

gluconate ion

N-formylanthranilate

selenocystathionine

imidazole-4-acetaldehyde

N-acetylneuraminic acid 9-phosphate

3-keto-beta-D-galactose

prostaglandin C2

vanillylmandelate

prostaglandin b1

3-oxohexanoyl-CoA

prostaglandin D1

L-4-hydroxyglutamic semialdehyde

11β-hydroxyandrostenedione

(3Z,6Z)-dodecadienoyl-CoA

5beta-cholestane-3alpha,7alpha-diol

2-amino-3-oxoadipic acid

dihydrolanosterol

L-xylonate

6-ketoprostaglandin f1α

3-oxooctanoyl-CoA

L-fucopyranose 1-phosphate

(2-trans,6-cis)-dodeca-2,6-dienoyl-CoA

S(8)-glutaryldihydrolipoamide

7alpha,12alpha-dihydroxycholest-4-en-3-one

2-hydroxyphenylacetic acid

3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestan-26-oyl-CoA

5beta-cholestane-3alpha,7alpha,26-triol

3-mercaptolactic acid

3-methyl-2-oxovalerate

N,N'-diacetylchitobiose

S(8)-(2-methylbutanoyl)dihydrolipoamide

chenodeoxycholoyl-CoA

5-hydroxykynurenamine

androsterone 3-glucosiduronic acid

testosterone 17-glucosiduronic acid

O-propanoylcarnitine (1-, no stereochemistry defined)

retinoyl β-glucuronide

prostaglandin F2beta

cholate

L-glutamate(1-)

L-aspartate(1-)

succinate dianion

linoleate

N-formyl-L-kynurenine

dihydrolipoate

orotate

indole-3-acetate

(S)-dihydroorotate

(-)-pipecolic acid

4-pyridoxate

8,9-EET

all-trans-retinoate

N-acetylneuraminate

L-α-aminobutyric acid

17beta-estradiol 3-glucosiduronic acid

3-hydroxyanthranilate

glyoxylate

phytanate

N-acetyl-L-glutamate(2-)

UTP(4-)

5-(2-carboxylatoethyl)-4-oxo-4,5-dihydro-1H-imidazol-5-ide

N(6)-(1,2-dicarboxylatoethyl)-AMP(4-)

dTDP-4-dehydro-6-deoxy-alpha-D-glucose(2-)

kynurenate

N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate(3-)

CMP(2-)

4-nitrophenyl phosphate(2-)

4-hydroxyestradiol

N-benzoylglycinate

19-hydroxytestosterone