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Table 2 Biological pathways displaying up-regulation (versus normal mucosa) in SPLs, LPLs, and CRCs

From: Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon

   Nominal p-values of enrichment scores †
Pathways n * N vs SPL N vs LPL N vs CRC
1) KEGG BASE EXCISION REPAIR 48 0.042 - -
2) KEGG HOMOLOGOUS RECOMBINATION 34 0.043 - -
3) REACTOME ACTIVATION OF THE PRE REPLICATIVE COMPLEX 35 0.047 - -
4) REACTOME HOMOLOGOUS RECOMBINATION REPAIR 22 - 0.048 -
5) BIOCARTA CELLCYCLE PATHWAY 32 - - 0.025
6) BIOCARTA MONOCYTE PATHWAY 20 - - 0.035
7) BIOCARTA P27 PATHWAY 14 - - 0.025
8) BIOCARTA RB PATHWAY 20 - - 0.047
9) BIOCARTA SET PATHWAY 15 - - 0.034
10) BIOCARTA SKP2E2F PATHWAY 12 - - 0.014
11) KEGG RNA POLYMERASE 27 - - 0.04
12) REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 40 - - 0.027
13) REACTOME CYTOSOLIC TRNA AMINOACYLATION 26 - - 0.031
14) REACTOME G1 PHASE 17 - - 0.03
15) REACTOME GLUCOSE TRANSPORT 55 - - 0.041
16) REACTOME GLYCOLYSIS 27 - - 0.039
17) REACTOME NEP NS2 INTERACTS WITH THE CELLULAR EXPORT MACHINERY 39 - - 0.049
18) REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY 9 - - 0.034
19) REACTOME PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 25 - - 0.027
20) REACTOME PROSTANOID HORMONES 15 - - 0.046
21) REACTOME RNA POLYMERASE III CHAIN ELONGATION 12 - - 0.033
22) REACTOME RNA POLYMERASE III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 21 - - 0.047
23) REACTOME TAT MEDIATED HIV1 ELONGATION ARREST AND RECOVERY 31 - - 0.049
24) REACTOME TRNA AMINOACYLATION 34 - - 0.048
25) REACTOME TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS 40 - - 0.043
26) REACTOME VPR MEDIATED NUCLEAR IMPORT OF PICS 48 - - 0.031
27) SA REG CASCADE OF CYCLIN EXPR 18 - - 0.01
28) BIOCARTA ARF PATHWAY 24 0.033 0.037 -
29) KEGG NUCLEOTIDE EXCISION REPAIR 48 0.031 0.043 -
30) KEGG ONE CARBON POOL BY FOLATE 19 0.004 0.032 -
31) REACTOME DUAL INCISION REACTION IN GG NER 18 0.032 0.025 -
32) REACTOME G2 M TRANSITION 80 0.038 0.035 -
33) REACTOME MITOCHONDRIAL TRNA AMINOACYLATION 11 0.032 0.04 -
34) REACTOME PURINE METABOLISM 42 0.037 0.03 -
35) REACTOME RNA POLYMERASE I CHAIN ELONGATION 29 0.021 0.026 -
36) REACTOME RNA POLYMERASE I PROMOTER ESCAPE 21 0.027 0.014 -
37) REACTOME RNA POLYMERASE I TRANSCRIPTION INITIATION 25 0.013 0.009 -
38) REACTOME RNA POLYMERASE I TRANSCRIPTION TERMINATION 22 0.027 0.013 -
39) REACTOME SNRNP ASSEMBLY 60 0.031 0.029 -
40) REACTOME MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE 11 0.015 - 0.029
41) REACTOME RNA POLYMERASE III TRANSCRIPTION INITIATION 29 0.041 - 0.047
42) REACTOME NUCLEAR IMPORT OF REV PROTEIN 39 - 0.049 0.043
43) REACTOME REV MEDIATED NUCLEAR EXPORT OF HIV1 RNA 41 - 0.043 0.039
44) BIOCARTA PTC1 PATHWAY 13 0.022 0.018 0.028
45) BIOCARTA RANMS PATHWAY 8 0.013 0.024 0.022
46) REACTOME CYCLIN A1 ASSOCIATED EVENTS DURING G2 M TRANSITION 19 0.038 0.034 0.026
47) REACTOME FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC 18 0.044 0.039 0.011
48) REACTOME PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS 13 0 0.004 0.008
49) REACTOME REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN 42 0.044 0.031 0.044
  1. * n = number of RefSeqs in the pathway.
  2. † measured by RS analysis; only significant p-values (< 0.05) are shown.