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Table 1 Annotation clusters with significantly enriched GO biological processes and pathways in PCB 153 treated samples a

From: Liver transcriptome analysis of Atlantic cod (Gadus morhua) exposed to PCB 153 indicates effects on cell cycle regulation and lipid metabolism

Category

Term

FDR

Gene/protein symbols

Annotation Cluster 1

Enrichment Score: 3.7

  

PANTHER_BP

Lipid, fatty acid and steroid metabolism

0

ACSA, AUHM, PQLC3, SCD5, HMDH, GNPAT, PCY2, UD11, STAR3, NSDHL, ACACA, SRBP1, FABP7N, ANXA4, PCTL, GDPD2, ACLY, PPARG, FABPL, DHB12

GOTERM_BP

Lipid metabolic process

0.2

ACSA, SCD5, APOH, HMDH, GNPAT, PCY2, KIT, UD11, GPAT3, STAR3, NSDHL, ACACA, SRBP1, BAX, PLB1, GDPD2, ACLY, MK14, PPARG, DHB12

GOTERM_BP

Lipid biosynthetic process

4.2

ACSA, GPAT3, STAR3, ACACA, NSDHL, SCD5, ACLY, HMDH, PCY2, DHB12

Annotation Cluster 2

Enrichment Score: 2.2

  

GOTERM_BP

DNA metabolic process

0

DNMT1, BAF, BLM, TYDP1, FEN1, NUP98, RTEL1, MCM3, PPIA, MCM5, RMI1, DPOA2, BAX, DPOD1, KC1E, FOS, PCNA, RECQ4

PANTHER_BP

DNA metabolism

0.1

MCM5, DPOA2, DNMT1, DPOD1, BLM, TYDP1, KC1E, FEN1, PCNA, RECQ4, RTEL1, MCM3

KEGG_PW

DNA replication

0.2

MCM5, DPOA, DPOD1, FEN1, PCNA, MCM3

REACT_PW

DNA Replication

0.2

MCM5, PSMD3, DPOA2, DPOD1, FEN1, PCNA, PSB7, MCM3

GOTERM_BP

DNA replication

0.5

MCM5, RMI1, DPOA2, DPOD1, BLM, FEN1, NUP98, PCNA. MCM3

PANTHER_BP

DNA repair

0.5

DPOD1, BLM, TYDP1, KC1E, FEN1, PCNA, RECQ4, RTEL1

GOTERM_BP

Cellular response to stress

0.9

SYAC, BLM, E2AK2, TYDP1, FEN1, RTEL1, ETV5, SRBP1, BAX, DPOD1, KC1E, MK14, FOS, PCNA, RECQ4

PANTHER_BP

DNA replication

1.1

MCM5, DPOA2, DPOD1, BLM, FEN1, PCNA, MCM3

GOTERM_BP

Cellular response to stimulus

1.8

SYAC, BLM, E2AK2, TYDP1, FEN1, RTEL1, ETV5, UD11, SRBP1, BAX, DPOD1, KC1E, ERBB3, MK14, PPARG, FOS, PCNA, RECQ4

GOTERM_BP

DNA-dependent DNA replication

3.0

MCM5, DPOD1, BLM, FEN1, MCM3

REACT_PW

Cell Cycle, Mitotic

4.5

MCM5, PSMD3, DPOA2, DPOD1, KC1E, KNTC1, FEN1, NUP98, PCNA, PSB7, MCM3

Annotation Cluster 3

Enrichment Score: 2.0

  

GOTERM_BP

Macromolecule localization

2.4

APOH, GNPTA, SNX12, KPCB, NUP98, SNX25, DVL1L, VPS53, STAR3, EZRI, SNX18, DPOA2, BAX, YIF1A, GOT1B, DUS16, APOM, PPARG, RFIP2, PCNA, FABL

  1. aEnrichment analysis was performed for functional categories GO BP (PANTHER_BP_ALL and GOTERM_BP_ALL) and pathway (KEGG and Reactome) using DAVID tools (functional annotation cluster). Only significant annotation terms (FDR < 5%) are shown. All the genes were up-regulated except four (KIT, UD11, PLB1, BAF, E2AK2), which were down regulated.