Table 1 The pathways found to be notable in the various analyses, and the most significant pathway that was not notable (listed last). A pathway is notable if the p-value is less than 0.0001 and the FDR is less than 0.01. A pathway is significant if the p-value is less than 0.05. The Status column gives the direction in which the pathway is found to be perturbed (activated or inhibited). The Signfct column contains an entry if the pathway is significant in the pan-cancer analysis. The entry is “N” if it is one of the notable pathways. Otherwise, it is “S”. A pathway has an asterisk if it is not notable in the pan-cancer analysis and previous studies have not linked it to the particular cancer

pan-cancer

Focal adhesion

5.99E-06

0.000789

Activated

N

PI3K-Akt signaling pathway

1.01E-05

0.000789

Activated

N

Rap1 signaling pathway

3.71E-05

0.001939

Activated

N

Calcium signaling pathway

4.95E-05

0.001942

Activated

N

Systemic lupus erythematosus

0.001966

0.05302

Activated

S

breast

ECM-receptor interaction

5.71E-05

0.008967

Activated

Complement and coagulation cascades

0.003855

0.218606

Activated

S

colon

Adrenergic signaling in cardiomyocytes*

3.35E-05

0.001709

Inhibited

S

Melanoma

3.68E-05

0.001709

Inhibited

S

Focal adhesion

4.73E-05

0.001709

Inhibited

N

Cytokine-cytokine receptor interaction

5.84E-05

0.001709

Activated

S

Pathways in cancer*

6.21E-05

0.001709

Inhibited

S

PI3K-Akt signaling pathway

6.53E-05

0.001709

Inhibited

N

Rap1 signaling pathway

0.002919

0.065477

Inhibited

N

glioblastoma

Cytokine-cytokine receptor interaction

5.12E-07

8.04E-05

Inhibited

S

Complement and coagulation cascades*

1.33E-05

0.000798

Inhibited

S

Systemic lupus erythematosus

1.94E-05

0.000798

Inhibited

S

PI3K-Akt signaling pathway

2.31E-05

0.000798

Inhibited

N

Chemokine signaling pathway

2.54E-05

0.000798

Inhibited

S

Vascular smooth muscle contraction

0.003076

0.069809

Inhibited

kidney

Rap1 signaling pathway

3.30E-06

0.000518

Inhibited

N

ECM-receptor interaction*

8.13E-06

0.000638

Inhibited

Colorectal cancer*

2.79E-05

0.001459

Inhibited

Focal adhesion

8.66E-05

0.0034

Inhibited

N

Insulin signaling pathway

0.000557

0.015232

Inhibited

glioma

Focal adhesion

4.94E-06

0.000674

Inhibited

T

ECM-receptor interaction*

8.59E-06

0.000674

Inhibited

Chemokine signaling pathway

1.74E-05

0.00091

Inhibited

S

Small cell lung cancer*

4.27E-05

0.001482

Inhibited

S

Cytokine-cytokine receptor interaction

4.72E-05

0.001482

Inhibited

S

Retrograde endocannabinoid signaling

0.000478

0.01252

Activated

Analysis

Pathway

p-value

FDR

Status

Signfct

lung adeno.

Chemokine signaling pathway

1.82E-08

2.86E-06

Activated

S

Cytokine-cytokine receptor interaction

1.51E-05

0.001187

Activated

S

Systemic lupus erythematosus

0.000108

0.005654

Activated

S

lung squamous

Chemokine signaling pathway

1.43E-05

0.002204

Activated

S

Cytokine-cytokine receptor interaction

4.14E-05

0.002204

Activated

S

Endocrine and other factor-reg. calcium reab.*

4.21E-05

0.002204

Inhibited

Amoebiasis

0.005649

0.221723

Inhibited

S

ovarian

Rap1 signaling pathway

4.02E-05

0.002785

Inhibited

N

PI3K-Akt signaling pathway

5.03E-05

0.002785

Inhibited

N

Calcium signaling pathway

5.32E-05

0.002785

Inhibited

N

Focal adhesion

0.000366

0.014354

Inhibited

N

rectum

Focal adhesion

3.63E-06

0.000342

Inhibited

N

Rap1 signaling pathway

4.36E-06

0.000342

Inhibited

N

Ras signaling pathway*

1.32E-05

0.000689

Inhibited

S

PI3K-Akt signaling pathway

4.96E-05

0.001727

Inhibited

N

Prostate cancer*

5.50E-05

0.001727

Inhibited

S

Melanoma

0.001514

0.039609

Inhibited

S

uterine

Focal adhesion

7.50E-07

0.000118

Inhibited

N

Maturity onset diabetes of the young

4.69E-05

0.003144

Activated

S

Calcium signaling pathway

6.01E-05

0.003144

Inhibited

N

Rap1 signaling pathway

0.005318

0.208728

Inhibited

N