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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.
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BMC Cancer

ISSN: 1471-2407

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