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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.