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Table 1 Analysis of the activity of the pathways by means of different approaches in the case-control comparison of early onset colorectal cancer

From: Understanding disease mechanisms with models of signaling pathway activities

  Circuits SEA   
PATHWAY Total Case Control UP vs DOWN UP vs ALL DOWN vs ALL GSEA SPIA
PPAR SIGNALING PATHWAY 106 3 19 DOWN ALL ALL DOWN* INH*
ERBB SIGNALING PATHWAY 139 11 2 UP UP DOWN DOWN* INH
CALCIUM SIGNALING PATHWAY 20 2 2 DOWN UP DOWN UP* ACT
NEUROACTIVE LIGAND-RECEPTOR INTERACTION 7 0 0 UP UP ALL UP* ACT
APOPTOSIS 28 0 0 DOWN ALL DOWN DOWN* INH
WNT SIGNALING PATHWAY 37 6 6 UP UP DOWN DOWN* INH
NOTCH SIGNALING PATHWAY 14 0 0 DOWN ALL ALL DOWN INH
VEGF SIGNALING PATHWAY 10 2 0 DOWN ALL ALL DOWN INH
CELL ADHESION MOLECULES 43 6 3 UP UP ALL UP* - 1
GAP JUNCTION 17 4 0 UP UP ALL UP* ACT
ANTIGEN PROCESSING AND PRESENTATION 6 0 0 DOWN ALL DOWN UP ACT
TOLL-LIKE RECEPTOR SIGNALING PATHWAY 103 0 0 UP UP DOWN UP* INH
JAK-STAT SIGNALING PATHWAY 7 7 0 DOWN ALL DOWN UP* INH
B CELL RECEPTOR SIGNALING PATHWAY 10 0 0 UP UP ALL UP* INH
Fc EPSILON RI SIGNALING PATHWAY 7 0 0 UP ALL ALL DOWN* INH
INSULIN SIGNALING PATHWAY 54 1 0 DOWN UP ALL DOWN* INH
GnRH SIGNALING PATHWAY 9 0 0 UP UP ALL DOWN* ACT
MELANOGENESIS 8 1 0 UP ALL ALL UP ACT
ADIPOCYTOKINE SIGNALING PATHWAY 31 0 2 DOWN ALL ALL UP INH
  1. 1 - This pathway is not implemented in SPIA.
  2. The first column contains the name of the pathway. The next three columns, collectively labeled as circuits, list the number of sub-pathways in the pathways (Total) and the number of them significantly activated in cases with respect to controls (Case) or vice versa (Control) in the comparison, respectively. The three next columns, collectively labeled as SEA, list the results of a conventional functional enrichment test [3] in three situations: UP vs DOWN) when the significantly upregulated genes are compared to the significantly downregulated genes, UP vs ALL) when significantly upregulated genes are compared to rest of genes, and DOWN vs ALL) when significantly downregulated genes are compared to the rest of genes. UP, DOWN and ALL means where the major part of the pathway lies in the comparison. Significantly up- and downregulated genes are obtained by a conventional t-test with multiple test adjustment as implemented in the Babelomics program [89]. Although the trends of the results are coincident with the other analyses, none of them resulted significant. The column labeled GSEA contains a version of GSEA test [15] implemented in the Babelomics program. The * and the boldface indicate the trend is significant according to the test. The last column, labeled as SPIA, contains the result of the application of the pathway impact analysis [23].