Table 3

Large-scale comparison between KEGG spider and GENECODIS

Input proteins/genes

GENECODIS

KEGG spider

Paper

Table

All

KEGG

k

max

Model

n

P-value

Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma [40]

Table 1: proteins found to be differentially expressed between matched normal and RCC primary lines

62

23

5

10

D₃

22

<0.01

Proteomic analysis of anaplastic lymphoma cell lines: identification of potential tumour markers [41]

Table 2: proteins overexpressed in FE-PD cells compared to SU-DHL-1 cells

41

13

3

3

D₂

12

0.015

Differential expression profiling of human pancreatic adenocarcinoma and healthy pancreatic tissue [42]

Table 3: proteins at higher levels in normal pancreas compared to pancreatic cancer

40

12

2

5

D₃

12

0.015

Proteomic search for potential diagnostic markers and therapeutic targets for ovarian clear cell adenocarcinoma [43]

Table 1: differentially expressed proteins in human ovarian cancer cells

36

17

3

4

D₂

13

0.025

Quantitative proteomic analysis to discover potential diagnostic markers and therapeutic targets in human renal cell carcinoma [44]

Table 3: differentially expressed proteins in RCC patients

91

36

12

14

D₂

33

<0.001

Protein profile changes in the human breast cancer cell line MCF-7 in response to SEL1L [45]

Table 4: MCF7-SEL1L differentially expressed genes identified by microarray analysis

60

9

1

4

D₂

7

0.03

Protein dysregulation in mouse hippocampus polytransgenic for chromosome 21 structures in the Down syndrome critical region [46]

Table 2: list of proteins dysregulated in hippocampus of polytransgenic micea

42

14

2

5

D₂

12

0.015

Differential expression of proteins in response to ceramide-mediated stress signal in colon cancer cells by 2-D gel electrophoresis and MALDI-TOF-MS [47]

Table 1: list of identified proteins on HCT116 2-DE gels

82

16

2

4

D₃

15

0.02

Subcellular proteome analysis of camptothecin analogue NSC606985-treated acute myeloid leukemic cells [48]

Table 2: functional classifications of the deregulated proteins in NSC606985-induced apoptotic NB4 Cellsa

88

15

1

5

D₃

15

<0.001

Proteome analysis of responses to ascochlorin in a human osteosarcoma cell line by 2-D gel electrophoresis and MALDI-TOF MS [49]

Table 2: differentially expressed proteins in ascochlorin-treated U2OS cells

87

13

3

5

D₂

12

<0.001

Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells [50]

Table 1: summary of differentially expressed proteins and their functional classifications

227

59

11

9

D₃

54

<0.001

Proteomic analysis of the resistance to aplidin in human cancer cells [51]

Table 1: differentially expressed proteins between resistant and wild-type HeLa cells identified in the membrane fraction

26

8

5

3

D₂

6

0.02

Proteomic analysis of the resistance to aplidin in human cancer cells [51]

Table 2: differentially expressed proteins between resistant and wild-type HeLa cells identified in the cytosolic fraction

37

11

5

7

D₂

11

0.015

Identification of specific protein markers in microdissected hepatocellular carcinoma

Table 2: identified proteins from HCC and nontumorous liver tissue by in-gel digestion and SELDI-MS

51

20

8

4

D₂

17

0.015

Comparison of membrane-associated proteins in human cholangiocarcinoma and hepatocellular carcinoma cell lines [52]

Table 1: list of proteins from the membrane fraction of HuCCA-1 and HCC-S102 cell lines which show up-regulated expression

56

11

2

5

D₃

11

<0.001

Contribution of laser microdissection-based technology to proteomic analysis in hepatocellular carcinoma developing on cirrhosis [53]

Table 1: proteins differentially expressed in tumorous LM-hepatocytes and total homogenates samples identified PMF

43

20

0

0

D₃

18

0.04

Proteome alterations induced in human white blood cells by consumption of Brussels sprouts: results of a pilot intervention study [54]

Table 1: protein alterations induced by a controlled dietary intervention with Brussels sprouts in human primary white blood cells

44

17

2

4

D₂

12

<0.05

The 'Paper' column reports the title of the paper that reported a list of differentially expressed proteins/genes related to different diseases or treated/untreated cell states. The 'Table' column reports the table number and legend from the paper. The 'Input proteins/genes' section reports the total number of proteins/genes (All) and the number (KEGG) that mapped to KEGG pathways. The 'GENECODIS' section reports results provided by GENECODIS; the 'k' column reports the number of pathways found to be enriched (p-value < 0.05); the 'max' column reports the number of input genes covered by the largest pathway. The 'KEGG spider' section reports results provided by KEGG spider; the 'Model' column specifies the most significant model (D₂ or D₃); the 'n' column reports the number of input proteins/genes covered by the model; the p-value column reports significance estimated by a Monte Carlo simulation procedure.

Antonov et al. Genome Biology 2008 9:R179   doi:10.1186/gb-2008-9-12-r179