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Table 3 Clustering of gene lists using functional annotations

From: Meta-analysis of Chicken – Salmonella infection experiments

Enrichment score (e) Enrichment score (et) (e)1 (et)1 (t-deduced)1 Content Focus
10.09 10.46 1 1 1 Lumen of organelles, specifically the nucleus
8.65 8.06 2 3 3 ATP / nucleotide binding; phosphorylation, (ser, thr) kinase, transferase, S_TKc
8.15 8.14 3 2 2 Mitochondrion (outer and inner membranes)
6.11 5.47 4 7 4-7 SH3 protein domain
5.94 6.30 5 5 5 Mitochondrion
5.31 5.93 6 6 6 Macromolecules, specifically protein catabolism, including UBL mechanism
5.00 6.42 7 4, 24 4-7, ± 20 Macromolecules / protein transport, especially import in nucleus / localization
4.83 4.28 8 8 8 Non-membrane bound organelles and cytoskeleton
4.31 3.95 9 10 9-10 Cell cycle (process)
4.12 3.57 10 13 ±15 actin cytoskeleton (binding)
3.94 3.18 11 19 ? Protein folding / Chaperone protein
3.90 3.85 12 11 11 Angiogenesis
3.73 3.69 13 12 12 Ubl conjugation
XXX 3.56 X 14 <10 Tyrosine phosphorylation
3.68 3.44 14 15 15 Endoplasmic reticulum
3.63 XXX 15 X X Ubiquitin / proteasome proteolysis
3.56 3.95 16 9 4-7 Transcription
3.52 3.22 17 17 17 GTPase activity
3.03 3.22 18 18 18 Muscle morphology
3.01 XXX 19 X X Intracellular vesicles
2.85 2.14 21 36 ? Cell-cell contacts
2.82 2.98 22 20 20 Protein modification and metabolism, including proteolysis
2.75 XXX 23 X X Protein domain WD (repeat)
2.70 2.31 24 31 ?  
2.70 2.68 25 23 23 Apoptosis
2.69 2.72 26 22 ±20 RRM (RNA recognition motif)
2.64 2.27 27 32 ? Macromolecule complexes, especially protein complexes
2.45 2.07 31 38 ±40 Lysosome
2.40 XXX 34 X X Cell movement
2.37 2.21 35 33 33 Mitochondrion / organelle outer membrane
2.21 1.67 36 52 ? Nucleotide binding via P-loop domain
2.08 1.94 38 41 41 Nuclear pore / RNA transport
2.05 2.14 39 37 37 Negative regulation of biosynthesis (nucleic acid, protein, macromolecules)
2.05 2.04 40 39 39 Cellular response to diverse stimuli
1.03 2.2 - 1.55 126 35 + 61 <40 Muscle proteins, skeletal muscle morphology proteins
  1. Clustering of the functional annotations of the gene lists of the differential expression (DE) group, i.e. the Number of Differentially Expressed genes (i.e. in the experiments and in the meta-analysis), and categories: (e): experiment - i.e. 4 studies, (t): time after infection – 14 different time point post-infection, and (et): overlap between the (e) and (t) groups. The t-values were deduced from the other groups because the number of data was too large for the DAVID software to analyze directly. 1: Number of the cluster within group.