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Table 2 Global comparison of the ontological categories differentially expressed in EGFR inhibitors-sensitive vs. resistant cell lines

From: Transcriptional changes associated with resistance to inhibitors of epidermal growth factor receptor revealed using metaanalysis

  All studies: Overexpressed in sensitive cells    Overexpressed in resistant cells  
  Term p-value   Term p-value
Table 2a
O Pathways in cancer 4.9E-15 T positive regulation of biosynthetic process 3.6E-17
MM plasma membrane part 7.7E-12 T positive regulation of cellular biosynthetic process 5.2E-17
CC regulation of cell proliferation 1.3E-10 T positive regulation of macromolecule Metabolic process 2.3E-16
MM endomembrane system 1.4E-10 R response to endogenous stimulus 8.9E-16
MM cell fraction 2.1E-09 T positive regulation of nitrogen compound Metabolic process 1.6E-15
A regulation of cell death 2.2E-09 T positive regulation of macromolecule biosynthetic process 9.3E-15
A regulation of programmed cell death 2.6E-09 CC regulation of cell proliferation 4.9E-14
Mt positive regulation of macromolecule Metabolic process 2.6E-09 R response to hormone stimulus 6.9E-14
CC cell proliferation 5.7E-09 R response to organic substance 9.6E-14
T protein complex biogenesis 7.0E-09 CC positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid Metabolic process 1.2E-13
Table 2b
A negative regulation of cell death 1.4E-07 A regulation of apoptosis 3.3E-10
AD cell migration 5.0E-08 A negative regulation of apoptosis 4.1E-10
AD cell adhesion 2.3E-07 A anti-apoptosis 8.1E-08
AD localization of cell 1.2E-06 CC cell cycle 8.2E-06
AD cell projection 3.2E-06 CC regulation of cell size 3.4E-05
AD Focal adhesion 4.3E-05 CY cytoskeletal protein binding 3.2E-06
CC negative regulation of cell proliferation 9.0E-05 CY actin cytoskeleton 1.0E-04
CC regulation of DNA Metabolic process 1.5E-04 DF negative regulation of cell differentiation 6.1E-06
CC mitotic cell cycle 5.9E-04 E regulation of oxidoreductase activity 5.1E-05
CC regulation of cell size 6.4E-04 E positive regulation of oxidoreductase activity 4.2E-04
IM response to wounding 4.4E-05 IM immune system development 1.8E-09
IM immune system development 6.2E-04 IM response to wounding 2.4E-08
IM T cell activation 6.8E-04 IM regulation of cytokine production 1.1E-07
IM humoral immune response 8.4E-04 IM positive regulation of immune system process 4.3E-06
M_c oligosaccharide Metabolic process 7.0E-04 IM positive regulation of cell activation 2.6E-05
M_l regulation of lipid Metabolic process 6.8E-06 IM inflammatory response 2.8E-05
M_l phosphoinositide Metabolic process 7.3E-05 IM wound healing 1.6E-04
M_l positive regulation of lipid Metabolic process 1.0E-04 IM immune response 1.8E-04
M_l lipid biosynthetic process 1.1E-04 IM defense response 4.5E-04
M_l phospholipid Metabolic process 2.3E-04 IM regulation of production of molecular mediator of immune response 9.1E-04
M_l cellular lipid catabolic process 4.2E-04 M_c monosaccharide Metabolic process 4.3E-06
M_l glycerolipid Metabolic process 5.4E-04 M_c hexose Metabolic process 1.2E-05
M_l glycerophospholipid Metabolic process 7.0E-04 M_c glucose Metabolic process 5.8E-05
M_l lipoprotein particle clearance 9.2E-04 M_c regulation of cellular ketone Metabolic process 2.0E-04
O Oncogenesis 3.4E-05 M_l regulation of lipid Metabolic process 2.6E-07
O ErbB signaling pathway 4.2E-04 M_l regulation of lipid biosynthetic process 1.1E-04
O Wnt signaling pathway 7.7E-04 M_l regulation of fatty acid Metabolic process 4.2E-04
    M_l positive regulation of lipid Metabolic process 4.9E-04
Legend:    MO regulation of cell motion 2.8E-12
A Apoptosis   O Pathways in cancer 2.8E-10
AD Adhesion   O regulation of DNA Metabolic process 1.2E-04
CC Cell cycle   O Ras protein signal transduction 2.1E-04
CY Cytoskeleton   O Oncogenesis 4.0E-04
DF Differentiation   R response to steroid hormone stimulus 6.2E-12
E Energy   R response to insulin stimulus 1.5E-07
Mt Metabolism   R response to vitamin 1.2E-06
IM Immunity   R response to lipopolysaccharide 1.8E-06
M_c Metabolism-carbohydrates   R response to glucocorticoid stimulus 2.6E-06
M_l Metabolism-lipids   R response to hydrogen peroxide 1.4E-05
MM Membrane   R cellular response to stress 3.1E-05
MO Motility   V regulation of angiogenesis 4.6E-06
O Oncogenesis   V myeloid leukocyte activation 4.4E-05
R Response to stimuli   V positive regulation of angiogenesis 4.2E-04
T Transcription/translation     
V Vasculogenesis     
Sensitive Resistant
Table 2c  
ErbB Signalling pathway Ras protein signal transduction
BCL2-associated agonist of cell death v-ral oncogene homolog A
mitogen-activated protein kinase 9 FERM, RhoGEF and pleckstrin domain
phosphoinositide-3-kinase beta nischarin
glycogen synthase kinase 3 beta IGF1 (somatomedin C)
c-abl oncogene 1 Rho GTPase activating protein 6
v-crk sarcoma virus CT10 X-associated ankyrin-containing protein
mitogen-activated protein kinase 8 ras homolog gene family, member A
ribosomal protein S6 kinase myosin IXB
mitogen-activated protein kinase 10 mitogen-activated protein kinase 1
phosphoinositide-3-kinase alpha GRB2-related adaptor protein 2
phospholipase C, gamma 1 Rho GTPase activating protein 5
CDK inhibitor 1A (p21, Cip1) soc-2 suppressor of clear homolog
epiregulin mitogen-activated protein kinase 14
v-myc oncogene homolog ropporin, rhophilin associated protein 1B
phosphoinositide-3-kinase subunit 5 r-ras oncogene homolog
v-erb-b2 oncogene homolog 2 CDC42 effector protein
v-aktoncogene homolog 1 fibroblast growth factor 2 (basic)
calcium/calmodulin-dep. protein kinase II G protein alpha 12
protein kinase C, alpha parathyroid hormone
neuregulin 1 GRB2-related adaptor protein
NCK adaptor protein 1 muscle RAS oncogene homolog
PTK2 protein tyrosine kinase 2 WAS protein family, member 2
phosphoinositide-3-kinase delta SHC transforming protein 1
betacellulin MAPKAP 2
ribosomal protein S6 kinase 2 Rho guanine nucleotide exchange factor 3
jun oncogene ATP-binding cassette, member 1
p21 (Cdc42/Rac)-activated kinase 2 cofilin 1 (non-muscle)
translation initiation factor 4E binding CDC42 effector protein 4
phospholipase C, gamma 2 neurofibromin 1
  neurotrophic tyrosine kinase, type 1
  ral GDF stimulator-like 2
  linker for activation of T cells
Sensitive Resistant
Table 2d  
Complement System
complement component 2 complement component 1, q A chain
complement component 3a receptor 1 complement component 1, q B chain
complement component 7 complement factor H
complement component 8, alpha  
complement component 8, beta  
complement component 9  
complement factor B  
complement factor H  
complement factor I  
Chemokines
chemokine (C-C motif) ligand 2 chemokine (C-C motif) ligand 13
chemokine (C-C motif) ligand 22 chemokine (C-C motif) ligand 19
chemokine (C-C motif) ligand 23 chemokine (C-C motif) ligand 2
chemokine (C-C motif) ligand 24 chemokine (C-C motif) ligand 20
chemokine (C-C motif) receptor 5 chemokine (C-C motif) ligand 8
  chemokine (C-C motif) receptor 5
  chemokine (C-X-C motif) ligand 1
  chemokine (C-X-C motif) ligand 13
  chemokine (C-X-C motif) ligand 6
Interleukins
interleukin 1, alpha interleukin 1 family, member 6
interleukin 10 interleukin 1, alpha
interleukin 2 receptor, alpha interleukin 1, beta
interleukin 6 (interferon, beta 2) interleukin 10
interleukin 8 interleukin 10 receptor, beta
  interleukin 13
  interleukin 22
  interleukin 5
  interleukin 6 (interferon, beta 2)
  interleukin 9
  1. The data represent the ontological and functional categories identified as overrepresented in the lists of differentially expressed genes, when compared to all genes in the human genome. The lists are provided by the DAVID analysis program [17,19]. a) Top ten categories with best p-values. b) Selected categories with p-value better than 10-4. For complete list of categories with p-values better than 10-4 see Additional file 3; the selected categories represent our choices as the ones that illustrate the best differences between resistant and sensitive cell lines. c) Genes expressed in ErbB signaling pathway and Ras protein signal transduction ontologies of sensitive and resistant cell lines respectively. d) Genes expressed in immune system development of sensitive versus resistant cell lines.