Table 3.
List of main pathways affected.
| Paper | Software | List of main pathways affected |
|---|---|---|
| Alter et al., 2011 | DAVID analysis | Alternative splicing, splice variant, zinc-finger, phosphoprotein, zinc, metal-binding, zinc-ion binding, dna-binding, ubiquitin mediated proteolysis, nucleus, transcription, transition metal ion binding, chromosomal rearrangement, ubl conjugation pathway, transcription regulation, coiled coil, regulation transcription, compositionally biased region: Ser-rich |
| Chien et al., 2013 | DAVID analysis | Long-term depression, Cytokine-cytokine receptor interaction, Vascular smooth muscle contraction, Arrhythmogenic right ventricular cardiomyopathy (ARVC), glycerophospholipid metabolism, allograft rejection, Jak-STAT signaling pathway, Hematopoietic cell lineage, Gap junction, T cell receptor signaling pathway, RIG-I-like receptor signaling pathways, Ubiquitin mediated proteolysis, Intestinal immune network for IgA production, Type II diabetes mellitus, Leukocyte transendothelial migration, GnRH signaling pathway |
| EMA (Easy Microarray data Analysis) | Long-term depression, Amoebiasis, Vascular smooth muscle contraction, Cytokine-cytokine receptor interaction, Arrhythmogenic right ventricular cardiomyopathy (ARVC), Intestinal immune network for IgA production, Endocytosis, Aldosterone-regulated sodium reabsorption, African trypanosomiasis, Graft-vs.-host disease | |
| GSEA Gene Set Enrichment Analysis | Arrhythmogenic right ventricular cardiomyopathy ARVC, terpenoid backbone biosynthesis, glycerophospholipid metabolism, vascular smooth muscle contraction, alpha linolenic acid metabolism, tight junction, inositol phosphate metabolism, cytosolic dna sensing pathway, renal cell carcinoma, cell receptor signaling pathway, chronic myeloid leukemia | |
| Chow et al., 2012 | ||
| Young autistic/control | MetaCore software suite | DNA damage-response, cell cycle and apoptosis-related pathways |
| DAVID analysis | DNA damage/cell cycle, apoptosis, and immune signaling and neurogenesis and neural development | |
| Adult autistic/control | MetaCore software suite | Cell differentiation, mitogenic signaling and apoptosis genes |
| All autistic and control cases independent of age | DNA-damage response, apoptosis and immune system response functions | |
| Enstrom et al., 2009 | DAVID analysis | NK function, cellular proliferation, and leukocyte function |
| Féron et al., 2016 | IPA analysis | Developmental disorders, gastrointestinal diseases, purine metabolism, inflammation |
| Garbett et al., 2008 | GSEA Gene Set Enrichment Analysis | Antigen-specific immune response, inflammation, cell death, autoimmune diseases, migration, and targeting of the immune response to specific cells |
| Ginsberg et al., 2012 | DAVID analysis | Mitochondrial oxidative phosphorylation, protein translation, synapse/neurotransmitters, vesicle transport, brain patterning, |
| IPA analysis | Oxidative phosphorylation | |
| Glatt et al., 2012 | DAVID analysis | Genes related to immune response, genes of the hemoglobin complex, and genes with guanine- or guanylate-binding affinity |
| Gregg et al., 2008 | DAVID analysis | Natural killer cell-mediated cytotoxicity |
| IPA analysis | Natural killer cell signaling, IL-2 signaling, serotonin receptor and dopamine receptor signaling, retinol and methionine metabolism | |
| Hu et al., 2006 | IPA analysis | Neurological development and function, neuronal signaling, extension of neurites, myelination, VEGF-induced release of nitric oxide, neurogenesis, survival of Purkinje cells, apoptosis of neurons, development of septum, TNF and other cytokines |
| Hu et al., 2009 | IPA analysis | Synaptic transmission, neurogenesis, neurulation, long-term potentiation (learning), protein ubiquitination, brain function, molecular and cellular functions, cell death, small molecule biochemistry, free radical scavenging, cellular function and maintenance, liver toxicity, circadian rhythm, and androgen sensitivity |
| Ivanov et al., 2015 | KEGG pathway analysis | Calcium signaling pathway, Amphetamine addiction, Leishmaniasis, GABAergic synapse, Retrograde endocannabinoid signaling, MAPK signaling pathway, Arrhythmogenic right ventricular cardiomyopathy (ARVC), Cholinergic synapse, GnRH signaling pathway, Glutamatergic synapse, Serotonergic synapse, Dopaminergic synapse, Steroid biosynthesis, Steroid biosynthesis, Wnt signaling pathway, Leukocyte transendothelial migration, Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy, Asthma, Influenza A, Carbohydrate digestion and absorption and Endocrine and other factor-regulated calcium reabsorption |
| Kong et al., 2013 | GSEA Gene Set Enrichment Analysis | Ribosome and spliceosome pathways, neuroactive ligand receptor interaction pathway, calcium signaling pathway, and Gap junction |
| Kuwano et al., 2011 | ||
| ASD/control group | IPA analysis | Cell morphology, cellular assembly and organization, nerve system development and function |
| asdMO/asdMO | IPA analysis | Cancer, RNA post-transcriptional modification, reproductive system disease, protein synthesis, immune functions |
| Mahfouz et al., 2015 | DAVID analysis | Synaptogenesis, regulation of apoptosis, regulation of cell death, GABAergic neurons, neuron projection, neuron differentiation, cell morphogenesis, learning/memory, behavior, mental retardation, epilepsy, mitochondrial function, protein translation, ubiquitination, synapse formation and elimination, protein turnover, ion channel, neurotransmitter receptor activity, and mitochondrial function |
| Nishimura et al., 2007 | DAVID analysis | Cell communication and signal transduction, immune response, defense response |
| IPA analysis | Cell cycle, cellular movement, and cell-to-cell signaling and interaction | |
| Pramparo et al., 2015 | Metacore GeneGo analysis | Apoptosis/Apoptotic nucleus, Immune response/Antigen presentation, Immune response/Phagocytosis, Immune Response/TCR signaling, Translation/Translation initiation, Inflammation/Interferon signaling, Apoptosis/Anti-Apoptosis via NF-kb, Cell Adhesion/Leukocyte chemotaxis, Inflammation/IFN-gamma signaling |
| Stamova et al., 2011 | IPA analysis | Cellular Assembly and organization, cellular compromise, small molecule biochemistry, vitamin and mineral metabolism, cell death, neuronal development, neuronal survival |
| Talebizadeh et al., 2014 | DAVID analysis | Protein-lipid modification |
| Tian et al., 2011 | IPA analysis | Immunological and inflammatory disease processes, cell-cell signaling, antigen presentation, cell cycle, development and growth, proliferation, mitochondrial dysfunction pathways |
| Voineagu and Eapen, 2013 | GO gene ontology enrichment analysis | Synaptic function, immune and inflammatory function |
| Walker et al., 2013 | ||
| Ileal Mucosa | PCA (Principal component analysis) | Gastrointestinal disease, inflammatory response, humoral immune response, tissue morphology, digestive system development and function, O-Glycan Biosynthesis, Propanoate Metabolism, Arginine and Proline Metabolism, and Alanine and Aspartate Metabolism |
| Colonic Mucosa | PCA (Principal component analysis) | Gastrointestinal disease, neurological disease, behavior, organ development, Atherosclerosis Signaling, Factors Promoting Cardiogenesis in Vertebrates and Mitotic Roles of Polo-Like Kinase |
| IPA analysis | Inflammatory disease, endocrine system development and function and digestive system development and function, Granzyme A Signaling, Athersclerosis Signaling, Valine, Leucine and Isoleucine Degradation and Clathrin-mediated Endocytosis Signaling | |
| Wen et al., 2016 | KEGG Pathway Analysis | MAPK signaling pathway, Calcium signaling pathway, Cell signaling, cell structure/transport, metabolism, neural, immune, cancer, cardiac disease, metabolic disease, Cell Adhesion Molecules, Wnt signaling pathway, mTOR signaling pathway, Focal adhesion, Regulation of actin cytoskeleton, Ubiquitin mediated proteolysis, Long-term potentiation, Axon guidance, and neurodegenerative diseases |
| Ziats and Rennert, 2013 | DAVID analysis | Extracellular matrix formation/glycoproteins, immune response, chromatin, and cell cytoskeleton |