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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

From: Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel

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

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BMC Genomics

ISSN: 1471-2164

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