Skip to main content

Table 3 Top 25 genes returned by the Animal PMT node using the GenMAPP Collagens pathway as a query. The horizontal line indicates the 50% recall point, above which half of the query genes are included.

From: A search engine to identify pathway genes from expression data on multiple organisms

Gene Producta

Symbol

P-valueb

Ac

Ed

Collagen, type IV, alpha 2

COL4A2

1.25E-09

ye

y

Nidogen

NID

1.42E-07

y

 

Actin binding LIM protein 1

ABLIM1

1.49E-07

  

Heparan sulfate proteoglycan 2

HSPG2

5.65E-07

y

y

Spectrin, alpha, non-erythrocytic 1

SPTAN1

7.97E-07

 

y

Osteonectin

SPARC

1.16E-06

y

 

Laminin, alpha 2

LAMA2

3.61E-06

y

 

Laminin, beta 1

LAMB1

4.89E-06

y

y

Collagen, type IV, alpha 5 (Alport Syndrome)

COL4A5

8.22E-06

y

 

Ataxin 2

ATXN2

1.01E-05

 

y

Adipocyte, C1Q and collagen domain Containing

ACDC

1.44E-05

 

n/a*

Laminin, gamma 1 (formerly LAMB2)

LAMC1

1.77E-05

y

y

Syntaxin binding protein 1

STXBP1

1.95E-05

 

y

Calumenin

CALU

2.24E-05

 

y

High density lipoprotein binding protein (vigilin)

HDLBP

2.33E-05

  

Crystallin, alpha B

CRYAB

2.41E-05

 

y

Collagen, type XV, alpha 1

COL15A1

2.53E-05

y

 

ATPase, H+ transporting, lysosomal accessory protein 1

ATP6AP1

2.57E-05

  

Procollagen-lysine, 2-oxoglutarate 5- dioxygenase 3

PLOD3

2.89E-05

  

Contactin 1

CNTN1

2.92E-05

  

AMP-activated protein kinase family member 5

ARK5

2.93E-05

  

Integrin, alpha 8

ITGA8

3.13E-05

 

n/a

Filamin A, alpha (actin binding protein 280)

FLNA

3.22E-05

 

y

Aminoadipate-semialdehyde synthase

AASS

3.46E-05

  

Spectrin, beta, non-erythrocytic 1

SPTBN1

3.49E-05

  
  1. aThe HUGO name for the gene. Genes in the original query set are italicized.
  2. bMSGR combined P value. This P value was not adjusted to reflect multiple testing; a Bonferroni correction could be applied by multiplying each by 11 to account for searches at each node in the PMT.
  3. cInvolved in cell – adhesion.
  4. dPredicted binding site for the EGR family of transcription factors.
  5. *n/a indicates that an upstream region could not be obtained for the given gene.
  6. eA "y" indicates that a gene had a positive hit for a particular field.