Construction and Analysis of Gene Co-Expression Networks in Escherichia coli
Abstract
:1. Introduction
2. Results
2.1. A Gene Co-Expression Network for E. coli Was Successfully Constructed
2.2. Each Module Performs Distinct Functions
2.3. E. coli Hub Gene Screening
2.4. Module-Based Analysis of Gene Expression Variation
2.5. Module-Based Analysis of Gene Connectivity
2.6. Modules That Correlate with Experimental Conditions
2.7. Comparison with Previous E. coli Networks
3. Discussion
4. Materials and Methods
4.1. Data Preparation
4.2. Weighted Gene Co-Expression Network Analysis (WGCNA)
4.3. Module-Based Qualitative and Quantitative analysis
4.4. Comparison of Gene Prediction Using Published Data
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Module (No. Probes) | GO Term (Benjamini-Adjusted p-Value) | KEGG (Adjusted p-Value) | ||
---|---|---|---|---|
Biological Process | Cellular Component | Molecular Function | ||
Black (3608) | Carbohydrate catabolic process (8.5 × 10−12) | Plasma membrane (4.9 × 10−30) | Cation binding (6.8 × 10−4) | Two-component system (3.7 × 10−31) |
Blue (1215) | Biological adhesion (3.6 × 10−2) | External encapsulation structure part (2.7 × 10−2) | — | Bacterial secretion system (3.4 × 10−17) |
Brown4 (30) | Siderophore metabolic process (3.1 × 10−5) | — | Iron transmembrane transporter activity (6.5 × 10−6) | Lysine degradation (4.5 × 10−4) |
Cyan (193) | Oxidation-reduction (9.3 × 10−4) | Anchored to membrane (2.9 × 10−2) | — | — |
Darkgreen (154) | — | — | Purine nucleoside binding (1.9 × 10−3) | Lipopolysaccharide biosynthesis (1.8 × 10−4) |
Darkgrey (78) | Lipopolysaccharide biosynthetic process (5.4 × 10−23) | Organelle inner membrane (8.3 × 10−3) | Cell surface antigen activity, host-interacting (8.5 × 10−29) | Lipopolysaccharide biosynthesis (1.2 × 10−11) |
Darkmagenta (48) | — | Viral capsid (2.0 × 10−5) | — | — |
Darkolivegreen (49) | Sulfate metabolic process (2.3 × 10−33) | — | Sulfate transmembrane transporter activity (2.1 × 10−5) | Sulfur metabolism (5.4 × 10−12) |
Darkorange (74) | Pathogenesis (2.1 × 10−5) | — | — | Pathogenic E. coli infection (6.7 × 10−9) |
Darkorange2 (999) | Phosphonate transport (2.5 × 10−6) | Peptidoglycan-based cell wall (5.9 × 10−11) | — | ABC transporters (3.8 × 10−15) |
Darkred (87) | Behavior (2.1 × 10−63) | Flagellum (4.1 × 10−51) | Motor activity (3.3 × 10−32) | Flagellar assembly (1.4 × 10−67) |
Darkturquoise (79) | Cellular amino acid biosynthetic process (1.4 × 10−66) | External encapsulating structure (1.2 × 10−2) | Acetolactate synthase activity (1.4 × 10−6) | Valine, leucine, and isoleucine biosynthesis (2.5 × 10−11) |
Green (678) | Translation (2.6 × 10−64) | Ribosome (2.4 × 10−59) | Structural constituent of ribosome (5.8 × 10−61) | Ribosome (2.4 × 10−56) |
Greenyellow (258) | peptidoglycan-based cell wall (2.1 × 10−2) | |||
Grey60 (101) | Iron ion transport (4.5 × 10−2) | — | Nucleoside binding (4.5 × 10−3) | ABC transporters (1.8 × 10−2) |
Ivory (35) | Transition metal ion transport (1.4 × 10−14) | — | Iron ion binding (2.5 × 10−10) | Biosynthesis of siderophore group nonribosomal peptides (3.4 × 10−10) |
Lightcyan1 (36) | Protein folding (4.2 × 10−6) | Zinc ion binding (9.2 × 10−4) | — | |
Lightyellow (93) | Fatty acid oxidation (1.7 × 10−2) | Peptidoglycan-based cell wall (2.3 × 10−2) | Acyl carrier activity (1.5 × 10−10) | Benzoate degradation via CoA ligation (3.0 × 10−2) |
Magenta (483) | Amine biosynthetic process (9.9 × 10−12) | Peptidoglycan-based cell wall (2.4 × 10−3) | Nucleoside binding (2.0 × 10−4) | Glycine, serine and threonine metabolism (1.2 × 10−4) |
Orangered4 (38) | Nitrogen compound biosynthetic process (2.8 × 10−24) | — | Anthranilate synthase activity (1.7 × 10−2) | Thiamine metabolism (4.4 × 10−10) |
Paleturquoise (56) | Glycerol metabolic process (6.3 × 10−7) | — | Glycerol-3-phosphate dehydrogenase activity (8.0 × 10−5) | Glycerophospholipid metabolism (1.4 × 10−3) |
Plum1 (40) | Anaerobic respiration (1.3 × 10−2) | Nitrate reductase complex (3.8 × 10−2) | — | — |
Sienna3 (46) | Anaerobic respiration (1.1 × 10−2) | — | Metal cluster binding (2.2 × 10−6) | Butanoate metabolism (1.5 × 10−5) |
Tan (295) | ncRNA metabolic process (4.3 × 10−13) | Plasma membrane (3.5 × 10−6) | RNA methyltransferase activity (7.1 × 10−5) | Mismatch repair (3.8 × 10−5) |
Module | Gene | Encoding Protein |
---|---|---|
Black | Z4148 | Hypothetical protein |
Blue | ECs1057 | Hypothetical protein |
Brown4 | fhuF | Ferric iron reductase protein |
Cyan | ECs2033 | Hypothetical protein |
Darkgreen | elaA | Hypothetical protein |
Darkgrey | rfbB | dTDP-glucose 4,6 dehydratase, NAD(P)-binding |
Darkmagenta | c1590 | Tail component of prophage |
Darkolivegreen | ssuC | Alkanesulfonate transporter permease |
Darkorange | ECs4574 | SepD |
Darkorange2 | c4484 | Aldolase |
Darkred | ECs2660 | Flagella biosynthesis protein FliZ |
Darkturquoise | ECs5231 | Ornithine carbamoyltransferase subunit I |
Green | rpsN | 30S ribosomal protein S14 |
Greenyellow | c0944 | Hypothetical protein |
Grey60 | ECs1840 | Hypothetical protein |
Ivory | fecR | Anti-sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA-bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
Lightcyan1 | ECs3950 | RNA polymerase sigma factor RpoD |
Lightyellow | pepN | Aminopeptidase |
Magenta | usg | Semialdehyde dehydrogenase |
Orangered4 | ECs1854 | OMP decarboxylase |
Paleturquoise | yagF | CP4-6 prophage |
Plum1 | yebT | MCE domain protein |
Sienna3 | ECs2379 | Hypothetical protein |
Tan | ECs4128 | Acetyl-CoA carboxylase biotin carboxylase subunit |
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Liu, W.; Li, L.; Long, X.; You, W.; Zhong, Y.; Wang, M.; Tao, H.; Lin, S.; He, H. Construction and Analysis of Gene Co-Expression Networks in Escherichia coli. Cells 2018, 7, 19. https://doi.org/10.3390/cells7030019
Liu W, Li L, Long X, You W, Zhong Y, Wang M, Tao H, Lin S, He H. Construction and Analysis of Gene Co-Expression Networks in Escherichia coli. Cells. 2018; 7(3):19. https://doi.org/10.3390/cells7030019
Chicago/Turabian StyleLiu, Wei, Li Li, Xuhe Long, Weixin You, Yuexian Zhong, Menglin Wang, Huan Tao, Shoukai Lin, and Huaqin He. 2018. "Construction and Analysis of Gene Co-Expression Networks in Escherichia coli" Cells 7, no. 3: 19. https://doi.org/10.3390/cells7030019
APA StyleLiu, W., Li, L., Long, X., You, W., Zhong, Y., Wang, M., Tao, H., Lin, S., & He, H. (2018). Construction and Analysis of Gene Co-Expression Networks in Escherichia coli. Cells, 7(3), 19. https://doi.org/10.3390/cells7030019