Table 5

Functional Annotation Enrichment analysis of statistically-significant under-expressed genes in European eel silver males from the river Tiber site (N = 8) in comparison with silver males from the lake Bolsena site (N = 7). FE = Fold Enrichment
Category Term Count PValue FE
KEGG_PATHWAY dre00190:Oxidative phosphorylation 32 <0.001 3.2
dre04540:Gap junction 8 0.003 3.8
dre03020:RNA polymerase 5 0.035 3.7
INTERPRO IPR003008:Tubulin/FtsZ, GTPase domain 7 <0.001 7.9
IPR017975:Tubulin, conserved site 7 <0.001 7.9
IPR000217:Tubulin 7 <0.001 7.9
IPR018316:Tubulin/FtsZ, 2-layer sandwich domain 7 <0.001 7.9
IPR004217:Mitochondrial inner membrane translocase complex, Tim8/9/10/13-zinc finger-like 4 0.005 9.0
IPR004217:Zinc finger, Tim10/DDP-type 4 0.005 9.0
IPR002453:Beta tubulin 4 0.005 9.0
IPR008011:Complex 1 LYR protein 4 0.012 7.2
IPR013838:Beta tubulin, autoregulation binding site 4 0.012 7.2
IPR003439:ABC transporter-like 5 0.018 4.5
IPR001648:Ribosomal protein S18 3 0.034 9.0
IPR017900:4Fe-4S ferredoxin, iron-sulphur binding, conserved site 3 0.034 9.0
IPR012677:Nucleotide-binding, alpha-beta plait 11 0.034 2.1
IPR003593:ATPase, AAA + type, core 8 0.042 2.4
SP_PIR ribosomal protein 29 <0.001 3.2
ribonucleoprotein 25 <0.001 3.5
mitochondrion 21 <0.001 3.1
ubiquinone 10 <0.001 4.0
transit peptide 10 <0.001 3.6
ribosome biogenesis 5 0.003 6.9
translocation 5 0.003 6.9
viral nucleoprotein 6 0.005 4.9
mitochondrion inner membrane 9 0.005 3.1
microtubule 7 0.009 3.6
chaperone 9 0.011 2.8
protein transport 8 0.016 2.9
iron-sulfur 4 0.027 5.5
iron 11 0.039 2.0
PIR_SUPERFAMILY PIRSF002306:tubulin 7 <0.001 8.5
GOTERM_MF GO:0005198 ~ structural molecule activity 41 <0.001 2.7
GO:0003735 ~ structural constituent of ribosome 25 <0.001 2.6
GO:0015078 ~ hydrogen ion transmembrane transporter activity 13 0.002 2.7
GO:0015077 ~ monovalent inorganic cation transmembrane transporter activity 14 0.002 2.5
GO:0009055 ~ electron carrier activity 15 0.001 2.6
GO:0016887 ~ ATPase activity 15 0.006 2.2
GO:0003723 ~ RNA binding 18 0.007 2.0
GO:0022890 ~ inorganic cation transmembrane transporter activity 14 0.008 2.2
GO:0015399 ~ primary active transmembrane transporter activity 9 0.009 2.9
GO:0015405 ~ P-P-bond-hydrolysis-driven transmembrane transporter activity 9 0.009 2.9
GO:0051536 ~ iron-sulfur cluster binding 6 0.012 4.0
GO:0051540 ~ metal cluster binding 6 0.012 4.0
GO:0016651 ~ oxidoreductase activity, acting on NADH or NADPH 7 0.020 3.1
GO:0046961 ~ proton-transporting ATPase activity, rotational mechanism 5 0.024 4.2
GO:0051537 ~ 2 iron, 2 sulfur cluster binding 3 0.032 9.2
GO:0003899 ~ DNA-directed RNA polymerase activity 5 0.032 3.9
GO:0034062 ~ RNA polymerase activity 5 0.032 3.9
GO:0008135 ~ translation factor activity, nucleic acid binding 9 0.032 2.3
GO:0003743 ~ translation initiation factor activity 7 0.037 2.7
GO:0003924 ~ GTPase activity 7 0.037 2.7
GOTERM_CC GO:0005739 ~ mitochondrion 43 <0.001 2.6
GO:0030529 ~ ribonucleoprotein complex 46 <0.001 2.3
GO:0044429 ~ mitochondrial part 31 <0.001 3.0
GO:0005740 ~ mitochondrial envelope 24 <0.001 2.8
GO:0005840 ~ ribosome 34 <0.001 2.2
GO:0043228 ~ non-membrane-bounded organelle 61 <0.001 1.6
GO:0043232 ~ intracellular non-membrane-bounded organelle 61 <0.001 1.6
GO:0005743 ~ mitochondrial inner membrane 19 <0.001 2.8
GO:0019866 ~ organelle inner membrane 19 <0.001 2.7
GO:0031966 ~ mitochondrial membrane 20 <0.001 2.6
GO:0031967 ~ organelle envelope 24 <0.001 2.3
GO:0031975 ~ envelope 24 <0.001 2.3
GO:0031090 ~ organelle membrane 24 0.001 1.9
GO:0031974 ~ membrane-enclosed lumen 22 0.002 1.9
GO:0005758 ~ mitochondrial intermembrane space 6 0.005 4.5
GO:0031970 ~ organelle envelope lumen 6 0.005 4.5
GO:0015934 ~ large ribosomal subunit 6 0.009 4.1
GO:0042719 ~ mitochondrial intermembrane space protein transporter complex 4 0.011 6.8
GO:0031980 ~ mitochondrial lumen 6 0.014 3.7
GO:0005759 ~ mitochondrial matrix 6 0.014 3.7
GO:0044455 ~ mitochondrial membrane part 6 0.021 3.4
GO:0033279 ~ ribosomal subunit 7 0.037 2.6
GO:0005874 ~ microtubule 7 0.037 2.6
GOTERM_BP GO:0006412 ~ translation 36 <0.001 2.5
GO:0042254 ~ ribosome biogenesis 10 <0.001 5.1
GO:0022613 ~ ribonucleoprotein complex biogenesis 10 <0.001 4.6
GO:0051258 ~ protein polymerization 7 <0.001 5.9
GO:0070585 ~ protein localization in mitochondrion 5 <0.001 9.2
GO:0006626 ~ protein targeting to mitochondrion 5 <0.001 9.2
GO:0007005 ~ mitochondrion organization 5 <0.001 9.2
GO:0006839 ~ mitochondrial transport 5 0.002 7.7
GO:0055085 ~ transmembrane transport 20 0.002 2.1
GO:0007006 ~ mitochondrial membrane organization 4 0.005 9.2
GO:0045039 ~ protein import into mitochondrial inner membrane 4 0.005 9.2
GO:0007007 ~ inner mitochondrial membrane organization 4 0.005 9.2
GO:0007018 ~ microtubule-based movement 7 0.005 4.0
GO:0006091 ~ generation of precursor metabolites and energy 16 0.005 2.1
GO:0007017 ~ microtubule-based process 8 0.011 3.1
GO:0022900 ~ electron transport chain 8 0.011 3.1
GO:0034660 ~ ncRNA metabolic process 9 0.012 2.7
GO:0006364 ~ rRNA processing 5 0.016 4.6
GO:0016072 ~ rRNA metabolic process 5 0.016 4.6
GO:0034622 ~ cellular macromolecular complex assembly 11 0.021 2.2
GO:0006886 ~ intracellular protein transport 11 0.029 2.1
GO:0034613 ~ cellular protein localization 11 0.029 2.1
GO:0034621 ~ cellular macromolecular complex subunit organization 11 0.029 2.1
GO:0006612 ~ protein targeting to membrane 4 0.031 5.3
GO:0065002 ~ intracellular protein transmembrane transport 3 0.032 9.2
GO:0070727 ~ cellular macromolecule localization 11 0.032 2.1
GO:0046907 ~ intracellular transport 13 0.037 1.9
GO:0034470 ~ ncRNA processing 6 0.037 3.1
GO:0065003 ~ macromolecular complex assembly 12 0.037 1.9
GO:0043623 ~ cellular protein complex assembly 7 0.038 2.7
GO:0015985 ~ energy coupled proton transport, down electrochemical gradient 7 0.038 2.7
GO:0034220 ~ ion transmembrane transport 7 0.038 2.7
GO:0015986 ~ ATP synthesis coupled proton transport 7 0.038 2.7
GO:0017038 ~ protein import 5 0.043 3.5
GO:0043933 ~ macromolecular complex subunit organization 12 0.047 1.9
UP_SEQ_FEATURE transit peptide:Mitochondrion 10 0.002 3.2
short sequence motif:Twin CX3C motif 3 0.036 8.6
SMART SM00382:AAA 8 0.009 3.2
SM00360:RRM 10 0.012 2.6
SM00651:Sm 4 0.042 4.8
COG_ONTOLOGY Translation, ribosomal structure and biogenesis 7 0.015 3.1

Pujolar et al.

Pujolar et al. BMC Genomics 2012 13:507   doi:10.1186/1471-2164-13-507

Open Data