1. Analysis of the common genes shared by GI microbiota and GC
1.1 The identification of the genes related to GI microbiota
10 metabolites of GI microbiota associated with gastric diseases were identified according to the HMDB database. These metabolites included Trimethylamine N-oxide, Butyric acid, Indoleacetic acid, Propionic acid, Indoxyl sulfate, p-Cresol, Acetone, Methane, 2-Methylerythritol and Glycine. 313 human genes associated with the 10 metabolites were identified by searching the STITCH database. The number of genes related to each metabolite is shown in Table 1.
Table 1
The metabolites of GI microbiota and associated gene number
HMDB ID | Name | Genes |
HMDB0000925 | Trimethylamine N-oxide | 36 |
HMDB0000039 | Butyric acid | 54 |
HMDB0000197 | Indoleacetic acid | 57 |
HMDB0000237 | Propionic acid | 59 |
HMDB0000682 | Indoxyl sulfate | 27 |
HMDB0001858 | p-Cresol | 25 |
HMDB0001659 | Acetone | 51 |
HMDB0002714 | Methane | 23 |
HMDB0011659 | 2-Methylerythritol | 9 |
HMDB0000123 | Glycine | 49 |
1.2 The identification of the genes related to GC
464 genes from OMIM database and 34 genes from GWAS Catalog were shown to associated with GC. No overlap was found in genes obtained from the two databases.
1.3 The common genes shared by GI microbiota and GC
33 genes were identified to be the common genes shared by GI microbiota and GC. The symbol and description of each gene is shown in Table 2.
Table 2
The common genes shared by gastric cancer and gastrointestinal microbiome
Gene | Full name of gene |
TRH | thyrotropin releasing hormone |
GNA11 | G protein subunit alpha 11 |
GNA12 | G protein subunit alpha 12 |
GNA14 | G protein subunit alpha 14 |
MTRNR2L2 | MT-RNR2 like 2 |
GNAI1 | G protein subunit alpha i1 |
GNAI3 | G protein subunit alpha i3 |
GNAO1 | G protein subunit alpha o1 |
MTOR | mechanistic target of rapamycin kinase |
GNAT1 | G protein subunit alpha transducin 1 |
GNAT2 | G protein subunit alpha transducin 2 |
GNAT3 | G protein subunit alpha transducin 3 |
BCAS2 | pre-mRNA-splicing factor |
GNB1 | G protein subunit beta 1 |
GNB2 | G protein subunit beta 2 |
GNB2L1 | guanine nucleotide-binding protein subunit beta-2-like 1 |
GNB3 | G protein subunit beta 3 |
GNB4 | G protein subunit beta 4 |
TRIO | trio Rho guanine nucleotide exchange factor |
GNG2 | G protein subunit gamma 2 |
GNG3 | G protein subunit gamma 3 |
GNG4 | G protein subunit gamma 4 |
GNG5 | G protein subunit gamma 5 |
GNG7 | G protein subunit gamma 7 |
TRIT1 | tRNAisopentenyltransferase 1 |
GNGT1 | G protein subunit gamma transducin 1 |
GNGT2 | G protein subunit gamma transducin 2 |
RSPO1 | R-spondin 1 |
GNG10 | G protein subunit gamma 10 |
GNG11 | G protein subunit gamma 11 |
GNG12 | G protein subunit gamma 12 |
GNG13 | G protein subunit gamma 13 |
PCSK9 | proprotein convertase subtilisin/kexin type 9 |
2. Gene ontology analysis of the common genes shared by GI microbiota and GC
Gene ontology analysis of 33 common genes shared by GI microbiota and GC conducted by WebGestalt is shown in Fig. 2. The main biological process in which the 33 common genes enriched include cell communication, response to stimulus, biological regulation, multicellular organismal process, metabolic process, cellular component organization and location. The main molecular function of these genes include protein binding, hydrolase activity, nucleotide binding, ion binding, nucleic acid binding, transferase activity and molecular transducer activity. The main cellular components that these genes enriched in include membrane, macromolecular complex, vesicle, cell projection, vacuole, cytosol, nucleus, endomembrane system and cytoskeleton.
3. Pathway analysis of the common genes shared by GI microbiota and GC
The pathway analysis was conducted by WebGestalt and ToppGene. The pathway enrichment analysis results are shown in Supplementary Table 1. The pathways of the common genes shared by GI microbiota and GC involve G-protein activation, Opioid Signalling, Protein folding, Platelet activation, signaling and aggregation, ADP signalling through P2Y purinoceptor 12, Regulation of insulin secretion, Morphine addiction, Retrograde endocannabinoid signaling, Glutamatergic synapse, Dopaminergic synapse, Apelin signaling pathway, Thromboxane signalling through TP receptor, ADP signalling through P2Y purinoceptor 1, Muscarinic acetylcholine receptor 2 and 4 signaling pathway, PI3K-Akt signaling pathway, Signal amplification, Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding, Thrombin signalling through proteinase activated receptors (PARs), Chaperonin-mediated protein folding, Prostacyclin signalling through prostacyclin receptor, G alpha (z) signalling events, G beta:gamma signalling through PLC beta, Adrenaline, noradrenaline inhibits insulin secretion, Presynaptic function of Kainate receptors, Glucagon-type ligand receptors, Opioid proopiomelanocortin pathway, Activation of Kainate Receptors upon glutamate binding, Opioid prodynorphin pathway, Ca2 + pathway, Enkephalin release, Cholinergic synapse, GABAergic synapse, Circadian entrainment, GABA B receptor activation, Activation of GABAB receptors, Glucagon-like Peptide-1 (GLP1) regulates insulin secretion, Cortocotropin releasing factor receptor signaling pathway, 5HT1 type receptor mediated signaling pathway, Vasopressin regulates renal water homeostasis via Aquaporins, Metabotropic glutamate receptor group II pathway, Opioid proenkephalin pathway, Integration of energy metabolism, Serotonergic synapse, G beta:gamma signalling through PI3Kgamma, Endogenous cannabinoid signaling, G alpha (12/13) signalling events, Heterotrimeric G-protein signaling pathway-rod outer segment phototransduction, G-protein beta:gamma signaling, Aquaporin-mediated transport, GABA receptor activation, Thyrotropin-releasing hormone receptor signaling pathway, Histamine H1 receptor mediated signaling pathway, G alpha (s) signalling events, Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell, 5HT2 type receptor mediated signaling pathway, G alpha (q) signalling events, G alpha (i) signalling events, Glucagon signaling in metabolic regulation, Histamine H2 receptor mediated signaling pathway, GABA-B receptor II signaling, G protein gated Potassium channels, Inhibition of voltage gated Ca2 + channels via Gbeta/gamma subunits, Activation of G protein gated Potassium channels, Oxytocin receptor mediated signaling pathway, Beta3 adrenergic receptor signaling pathway, Alcoholism, Beta-catenin independent WNT signaling, 5HT4 type receptor mediated signaling pathway, Inwardly rectifying K + channels, Platelet homeostasis, Class B/2 (Secretin family receptors), Transmission across Chemical Synapses, Chemokine signaling pathway, Muscarinic acetylcholine receptor 1 and 3 signaling pathway, Heterotrimeric G-protein signaling pathway-Gq alpha and Go alpha mediated pathway, Pathways in cancer, Beta1 adrenergic receptor signaling pathway, Beta2 adrenergic receptor signaling pathway, GPCR downstream signaling, Signaling by GPCR, Signaling by Wnt, Neuronal System, Hemostasis, Gastrin-CREB signalling pathway via PKC and MAPK, PI3 kinase pathway, Angiotensin II-stimulated signaling through G proteins and beta-arrestin, Ras signaling pathway, Metabotropic glutamate receptor group III pathway, Potassium Channels, Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway, GPCR ligand binding, Dopamine receptor mediated signaling pathway, Wnt signaling pathway, Metabolism of proteins, Sphingosine 1-phosphate (S1P) pathway, Transmembrane transport of small molecules, S1P2 pathway, S1P3 pathway, Inflammation mediated by chemokine and cytokine signaling pathway, PLC beta mediated events, G-protein mediated events, S1P5 pathway, Alzheimer disease, S1P4 pathway, Long-term depression, Phototransduction, CXCR3-mediated signaling events, Thrombin signaling and protease-activated receptors, Activation of the phototransduction cascade, Bioactive Peptide Induced Signaling Pathway, Chagas disease (American trypanosomiasis), Inhibition of adenylate cyclase pathway, Adenylate cyclase inhibitory pathway, S1P1 pathway, Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1), Aspirin Blocks Signaling Pathway Involved in Platelet Activation, Incretin synthesis, secretion, and inactivation, Visual signal transduction: Cones, Visual signal transduction: Rods, CXCR4 Signaling Pathway, Intracellular Signalling Through Prostacyclin Receptor and Prostacyclin, Vasopressin Regulation of Water Homeostasis, Intracellular Signalling Through PGD2 receptor and Prostaglandin D2, Phospholipids as signalling intermediaries, Nicotine pharmacodynamics pathway, Excitatory Neural Signalling Through 5-HTR 4 and Serotonin, Corticotropin Activation of Cortisol Production, PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase, How Progesterone Initiates Oocyte Membrane, Signaling Pathway from G-Protein Families, Inactivation, recovery and regulation of the phototransduction cascade, Excitatory Neural Signalling Through 5-HTR 7 and Serotonin, The phototransduction cascade, and Rapid glucocorticoid signaling.
4. Analysis of interaction networks of the common genes shared by GI microbiota and GC
The 33 common genes shared by GI microbiota and GC were further analyzed by GeneMANIA, and the interaction networks were mapped by Cytoscape software (Fig. 3). Each node represents a particular gene. The color of the gene represents a kind of biological function. Here show the 7 main functions of the common genes, including heterotrimeric G-protein complex, extrinsic component of cytoplasmic side of plasma membrane, G-protein beta/gamma-subunit complex binding, extrinsic component of plasma membrane, extrinsic component of membrane, GTPase activity, response to glucagon. Each line of a color indicates a kind of interaction. The detail of the interactions is in Table 3.
Table 3
The interaction patterns and their proportions of protein
Network Categories | Percentage |
Shared protein domains | 45.34% |
Physical Interactions | 34.19% |
Predicted | 12.40% |
Pathway | 6.50% |
Co-expression | 1.21% |
Co-localization | 0.36% |