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. Author manuscript; available in PMC: 2012 May 6.
Published in final edited form as: J Proteome Res. 2011 Mar 30;10(5):2425–2439. doi: 10.1021/pr101245u

Table 1. Regulation of the overrepresented GO terms and KEGG pathways.

The values in bold are statistically significant (see Methods).

Groups of pair-wise comparison among the samples
I II III IV V VI
Description of the overrepresented
GO terms and KEGG pathways		 ΦMφ,avg/ΦDC,avg ΦMφ,KO/ΦDC,KO ΦMφ,H37Rv/ΦDC,H37Rv ΦMφ,BCG/ΦDC,BCG ΦMφ,KO/ΦMφ,H37Rv ΦMφ,KO/ΦMφ,BCG ΦMφ,H37Rv/ΦMφ,BCG ΦDC,KO/ΦDC,H37Rv ΦDC,KO/ΦDC,BCG ΦDC,H37Rv/ΦDC,BCG WCMφ/ΦMφ,avg WCDC/ΦDC,avg WCMφ/WCDC
Cluster 1
MITOCHONDRIAL INNER MEMBRANE −1.20 1.09 0.77 −1.21 1.20 0.93 −1.14 0.94 −1.38 −1.60 −1.16 1.29 1.90
ORGANELLE INNER MEMBRANE −1.11 1.05 0.91 −1.14 1.24 0.93 −1.21 1.07 −1.29 −1.62 −1.14 1.20 1.91
MITOCHONDRIAL MEMBRANE −1.18 0.91 0.80 −1.30 1.16 0.98 −1.10 0.99 −1.41 −1.73 −1.19 1.32 1.88
MITOCHONDRIAL ENVELOPE −1.13 0.95 0.78 −1.27 1.19 1.02 −1.08 0.96 −1.42 −1.70 −1.20 1.22 1.84
Cluster 2
ELECTRON TRANSPORT CHAIN −1.54 0.86 −0.69 −1.26 1.01 −0.88 −1.00 0.61 −1.51 −1.68 −0.79 1.09 1.21
GENERATION OF PRECURSOR METABOLITES AND ENERGY 0.68 1.19 −0.94 −1.25 1.39 1.22 −1.20 0.81 −1.50 −1.38 −0.58 0.86 1.24
OXIDATION REDUCTION −0.89 1.21 0.84 −1.26 1.08 1.28 −0.82 −1.05 −1.49 −1.50 1.00 −1.12 1.00
Cluster 3
STRUCTURAL CONSTITUENT OF RIBOSOME 1.06 0.89 −0.79 1.57 1.56 1.23 −1.48 1.10 1.02 −0.88 1.01 −0.83 1.65
RIBOSOME 1.14 1.06 −0.82 1.46 1.55 1.52 −1.41 0.97 0.97 −0.91 0.71 −0.95 1.68
TRANSLATION 1.08 0.92 −1.34 1.51 1.51 1.12 −1.44 1.13 1.20 1.10 1.01 0.83 1.48
RIBONUCLEOPROTEIN COMPLEX 1.34 0.98 −1.07 1.77 1.58 1.13 −1.52 1.16 1.47 1.04 0.79 −1.07 1.32
Cluster 4
CELLULAR RESPIRATION 0.65 1.37 0.76 −1.29 1.42 1.33 −0.96 0.73 −1.58 −1.66 −0.47 0.98 1.78
ENERGY DERIVATION BY OXIDATION OF ORGANIC COMPOUNDS 0.70 1.52 −0.83 −1.54 1.56 1.62 −0.88 0.64 −1.64 −1.50 0.64 0.88 1.67
Cluster 5
CYTOSKELETON −1.74 −1.41 −1.31 −0.79 0.73 −0.76 −0.56 0.83 1.10 1.05 0.83 1.21 −1.01
Cluster 6
INTRACELLULAR PROTEIN TRANSPORT 1.60 1.06 1.02 1.19 0.96 0.73 −1.02 0.58 0.78 −0.73 −1.12 −1.99 −1.13
CELLULAR PROTEIN LOCALIZATION 1.55 1.00 0.97 1.17 0.93 −0.79 −1.00 0.55 0.76 −0.73 −1.17 −1.93 −1.11
CELLULAR MACROMOLECULE LOCALIZATION 1.53 1.00 0.96 1.19 0.96 −0.79 −1.00 0.55 0.75 −0.73 −1.19 −1.95 −1.09
INTRACELLULAR TRANSPORT 1.55 1.12 1.23 1.00 0.83 0.79 −0.72 −0.97 −0.80 −0.72 −1.36 −1.78 −0.86
PROTEIN TRANSPORT 1.62 1.12 0.99 1.51 1.05 −1.17 −1.26 −0.99 0.84 −0.70 −0.87 −1.62 −1.02
ESTABLISHMENT OF PROTEIN LOCALIZATION 1.56 1.08 0.99 1.50 1.02 −1.25 −1.25 −0.95 0.81 −0.69 −0.91 −1.65 −1.02
Cluster 7
ACTIN CYTOSKELETON ORGANIZATION −1.58 −1.91 −1.64 1.02 0.81 −0.94 −0.96 1.03 1.78 1.05 −1.07 −1.01 −1.60
ACTIN FILAMENT-BASED PROCESS −1.71 −1.94 −1.70 0.95 0.77 −0.83 −0.91 1.03 1.72 1.00 −1.14 −1.00 −1.46
CYTOSKELETON ORGANIZATION −1.59 −1.57 −1.69 −0.99 0.89 −0.65 −0.74 −0.76 1.29 1.22 −0.99 −1.03 −1.52
Cluster 8
ACTIN CYTOSKELETON −2.03 −1.46 −1.72 −0.98 1.13 0.73 −0.70 0.89 1.44 1.04 −0.92 1.05 −1.32
ACTIN BINDING −2.20 −1.68 −1.81 0.72 1.00 −0.85 −0.83 0.86 1.57 1.14 −0.66 −1.08 −1.61
CYTOSKELETAL PROTEIN BINDING −2.16 −1.68 −1.85 −0.83 0.94 −0.83 −0.79 0.82 1.46 1.16 0.80 −1.04 −1.66
CYTOSKELETAL PART −1.74 −1.12 −1.48 −0.82 0.84 1.00 0.71 −0.97 1.10 1.28 −0.97 1.23 −0.90
Cluster 9
CELL CORTEX −1.36 −1.21 −1.22 0.93 0.93 −1.16 −0.60 1.06 1.29 1.26 −1.29 −1.15 −1.13
Cluster 10
HYDROGEN ION TRANSMEMBRANE TRANSPORTER ACTIVITY 0.74 0.66 0.71 0.71 0.76 −1.05 −1.22 −1.09 −1.44 −1.10 −1.37 0.92 1.56
MONOVALENT INORGANIC CATION TRANSMEMBRANE TRANSPORTER ACTIVITY 0.65 −0.72 0.85 −0.90 0.61 −1.00 −1.10 −1.08 −1.54 −1.06 −1.56 0.79 1.56
INORGANIC CATION TRANSMEMBRANE TRANSPORTER ACTIVITY 0.57 0.73 0.82 0.75 0.91 −0.58 −1.11 0.86 −1.18 −1.02 −1.28 0.97 1.61
Cluster 11
MRNA PROCESSING 1.54 0.92 0.96 1.62 1.44 −1.18 −1.45 1.13 1.32 1.00 −1.02 −1.03 0.63
RNA PROCESSING 1.46 0.74 1.01 1.75 1.38 −1.26 −1.49 1.18 1.31 1.01 −0.97 −1.00 0.68
Cluster 12
RESPIRATORY CHAIN −1.99 −1.40 −1.20 −1.42 0.75 −1.37 −1.23 0.66 −1.68 −1.52 −0.83 0.96 1.31
Cluster 13
ENDOPLASMIC RETICULUM MEMBRANE 1.36 0.92 −0.89 1.06 0.80 −0.84 −0.88 −0.82 0.86 0.86 −1.08 1.23 1.81
NUCLEAR ENVELOPE-ENDOPLASMIC RETICULUM NETWORK 1.39 1.05 −0.64 1.24 0.94 −0.78 −0.94 0.63 0.88 0.81 −1.05 0.99 1.70
ENDOPLASMIC RETICULUM PART 1.46 0.93 1.25 1.20 0.49 −0.96 −0.75 0.83 0.71 −0.80 1.58 1.36 1.07
Cluster 14
MICROSOME 1.09 1.24 0.80 0.65 1.26 0.93 −0.90 1.00 −0.68 −0.97 −1.65 −1.12 1.46
VESICULAR FRACTION 1.10 1.26 0.81 0.64 1.26 0.91 −0.89 1.00 −0.69 −0.95 −1.65 −1.11 1.48
MEMBRANE FRACTION 1.11 0.96 0.90 1.25 1.37 0.68 −1.19 1.16 1.33 0.98 −1.84 −0.76 1.44
INSOLUBLE FRACTION 1.14 1.00 −0.85 1.22 1.31 0.78 −1.23 1.19 1.31 0.91 −1.77 −0.77 1.49
CELL FRACTION 1.25 1.11 −0.85 1.19 1.32 0.85 −1.21 1.04 1.19 0.90 −1.72 −0.67 1.55
Cluster 15
REGULATION OF CELLULAR COMPONENT SIZE −1.55 −1.43 −1.18 0.86 1.19 −1.07 −0.86 1.27 1.53 −0.81 0.67 1.17 −0.84
Cluster 16
CHROMATIN 0.64 0.95 −1.42 1.29 1.16 −0.83 −1.15 0.89 0.87 −0.86 −1.37 −1.51 1.05
CELLULAR MACROMOLECULAR COMPLEX ASSEMBLY 1.02 1.51 −1.17 1.21 1.35 0.97 −1.10 −1.27 0.84 1.24 −0.96 −1.65 −0.97
CELLULAR MACROMOLECULAR COMPLEX SUBUNIT ORGANIZATION 0.93 1.42 −1.15 1.20 1.32 0.88 −1.08 −1.17 0.81 1.13 −0.92 −1.60 −1.02
MACROMOLECULAR COMPLEX ASSEMBLY 1.09 1.69 −1.16 1.15 1.35 1.09 −1.07 −1.33 0.73 1.27 −1.00 −1.62 −0.96
MACROMOLECULAR COMPLEX SUBUNIT ORGANIZATION 1.06 1.69 −1.12 1.14 1.36 1.08 −1.05 −1.32 0.73 1.22 −1.00 −1.56 −1.00
Cluster 17
LYSOSOME 1.70 1.65 1.48 1.16 1.16 −0.70 −1.05 −0.80 −1.26 −0.73 0.99 −1.06 0.76
LYTIC VACUOLE 1.72 1.66 1.50 1.15 1.19 −0.69 −1.04 −0.84 −1.23 −0.74 1.00 −1.05 0.75
VACUOLE 1.81 1.76 1.40 1.11 1.20 −0.66 −0.99 −0.78 −1.35 −0.84 0.91 −1.04 0.87
Cluster 18
HEMOPOIESIS −1.26 −1.06 −1.04 0.91 −1.30 −1.40 −1.04 0.84 −0.95 −0.83 −0.78 1.05 0.78
HEMOPOIETIC OR LYMPHOID ORGAN DEVELOPMENT −1.37 −1.28 −1.28 1.03 −1.24 −1.46 −1.19 −0.97 0.93 −0.69 −0.74 0.95 0.76
Cluster 19
MEMBRANE ORGANIZATION 1.26 0.72 −0.94 1.09 0.81 −0.48 −1.06 0.95 0.83 −0.64 −1.06 −1.24 1.72
VESICLE-MEDIATED TRANSPORT 1.38 0.86 1.00 1.25 0.95 −1.01 −1.02 0.77 0.98 0.64 −1.20 −1.33 1.64
Cluster 20
CELLULAR HOMEOSTASIS 0.59 0.76 0.92 −0.79 −0.87 0.89 −0.75 1.36 0.95 −1.07 1.72 −0.66 −0.74
Cluster 21
ALZHEIMER'S DISEASE (KEGG) −1.46 −1.01 −0.97 −1.18 0.83 −0.86 −1.20 0.74 −1.46 −1.41 −1.31 0.90 1.80
OXIDATIVE PHOSPHORYLATION (KEGG) −1.57 −0.71 −1.05 −1.33 0.93 −0.78 −1.22 0.81 −1.80 −1.61 −1.13 0.99 1.56
PARKINSON'S DISEASE (KEGG) −1.31 −0.68 −1.15 −1.17 0.89 −1.09 −1.43 −0.91 −1.62 −1.39 −1.27 0.83 1.95
HUNTINGTON'S DISEASE (KEGG) −1.10 0.72 −0.76 −1.11 0.99 −0.90 −1.32 0.64 −1.57 −1.43 −1.47 0.74 1.96
Cluster 22
ANTIGEN PROCESSING AND PRESENTATION (KEGG) 1.69 1.47 0.85 1.27 1.23 0.68 −1.12 0.89 0.91 1.04 1.65 1.15 0.92