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Table 4 Summary list of proteins/genes belonging to selected functional groups to which differentially expressed tags were annotated

From: Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish

Category

Differentially expressed transcript (tag) annotation

Calcium binding proteins (CaBP)

ACTN3, α actinin 3

MYL4, Myosin light chain 4 *

 

AT2A1, Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

MYL6, Myosin light polypeptide 6

 

CAN2, Calpain-2 catalytic subunit *

PERE, Eosinophil peroxidase

 

CASQ1, Calsequestrin-1

PERF, Perforin-1

 

CLC4 M, C-type lectin domain family 4 member M

PRVB, Parvalbumin β *

 

CPNS1, Calpain small subunit 1 *

S10A5, Protein S100-A5

 

CRP, C-reactive protein

S10AD, Protein S100-A13 *

 

DNSL3, Deoxyribonuclease gamma

S10I, Ictacalcin

 

ELA1, Elastase-1

SCUB2, Signal peptide, CUB and EGF-like domain-containing protein 2

 

ENTK, Enteropeptidase

SRCA, Sarcalumenin

 

EVPL, Envoplakin

TITIN, Titin

 

FBLN5, Fibulin-5

TKTL1, Transketolase-like protein 1

 

HORN, Hornerin

TNNC1, Troponin C, slow skeletal and cardiac muscles

 

MLE3, Myosin light chain 3, skeletal muscle isoform *

TNNC2, Troponin C, skeletal muscle

 

MLRS, Myosin regulatory light chain 2, skeletal muscle isoform *

YRK, Proto-oncogene tyrosine-protein kinase Yrk

Transcription factors (TF)

CEBPA, CCAAT/enhancer-binding protein α

JUN, Transcription factor AP-1

 

DMRT1, Doublesex- and mab-3-related transcription factor 1

JUND, Transcription factor jun-D

 

EGR1, Early growth response protein 1

KLF10, Krueppel-like factor 10

 

ETV6, Transcription factor ETV6

MED21, Mediator of RNA polymerase II transcription subunit 21

 

FOS, Proto-oncogene protein c-fos

NDK, Nucleoside diphosphate kinase

 

HM20B, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related

USF2, Upstream stimulatory factor 2

 

JAD1B, Histone demethylase JARID1B

YBOX1, Nuclease-sensitive element-binding protein 1

Other regulators of transcription

DNMT1, DNA (cytosine-5)-methyltransferase 1

RAN, GTP-binding nuclear protein Ran

 

FUBP2, Far upstream element-binding protein 2

SMYD1, SET and MYND domain-containing protein 1

 

HSBP1, Heat shock factor-binding protein 1

TNNI2, Troponin I, fast skeletal muscle

 

LEP, Leptin

TRI16, Tripartite motif-containing protein 16

 

MURC, Muscle-related coiled-coil protein

TXNIP, Thioredoxin-interacting protein

 

NC2B, Protein Dr1

UBIQ, Ubiquitin

 

PAR15, Poly [ADP-ribose] polymerase 15

ZEP1, Zinc finger protein 40

Components of signal transduction pathways/intracellular signaling

1433B, 14-3-3 protein β/α

MK12, Mitogen-activated protein kinase 12

 

ACHA4, Neuronal acetylcholine receptor subunit α 4

P2RY8, P2Y purinoceptor 8

 

APOEB, Apolipoprotein Eb

PA24C, Cytosolic phospholipase A2 gamma

 

ARF4, ADP-ribosylation factor 4

PARPT, TCDD-inducible poly [ADP-ribose] polymerase

 

ARHGJ, Rho guanine nucleotide exchange factor 19

PDK4, Pyruvate dehydrogenase [lipoamide] kinase isozyme 4, mitochondrial

 

ARL1, ADP-ribosylation factor-like protein 1

PIN1, Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

 

C42S1, CDC42 small effector protein 1

RAB7A, Ras-related protein Rab-7a

 

CAP1, Adenylyl cyclase-associated protein 1

RAC2, Ras-related C3 botulinum toxin subste 2

 

CEBPA, CCAAT/enhancer-binding protein α (TF)

RAN, GTP-binding nuclear protein Ran

 

CLC4 M, C-type lectin domain family 4 member M

RGS1, Regulator of G-protein signaling 1

 

CML1, Chemokine receptor-like 1

RGS2, Regulator of G-protein signaling 2

 

CNIH, Protein cornichon homolog

RND2, Rho-related GTP-binding protein RhoN

 

CO1A1, Collagen α1(I) chain

S10I, Ictacalcin

 

CO1A2, Collagen α2(I) chain

SCUB2, Signal peptide, CUB and EGF-like domain-containing protein 2

 

EBI2, EBV-induced G-protein coupled receptor 2 homolog

SOCS3, Suppressor of cytokine signaling 3

 

EPHA2, Ephrin type-A receptor 2

STMN1, Stathmin

 

FIBP, Acidic fibroblast growth factor intracellular-binding protein

TACD2, Tumor-associated calcium signal transducer 2

 

FOS, Proto-oncogene protein c-fos (TF)

TITIN, Titin

 

GRN, Granulins

TRI16, Tripartite motif-containing protein 16

 

HG2A, HLA class II histocompatibility antigen gamma chain

UROK, Urokinase-type plasminogen activator

 

HINT1, Histidine triad nucleotide-binding protein 1

VANG2, Vang-like protein 2

 

IMPA1, Inositol monophosphatase

YRK, Proto-oncogene tyrosine-protein kinase Yrk

 

JUN, Transcription factor AP-1 (TF)

 
 

KLF10, Krueppel-like factor 10 (TF)

 
 

MGST3, Microsomal glutathione S-transferase 3

 

Ion transporters and other proteins related to ion homeostasis or osmoregulation

ACHA4, Neuronal acetylcholine receptor subunit α4

CLIC4, Chloride intracellular channel protein 4

 

AQP3, Aquaporin-3

COX17, Cytochrome c oxidase copper chaperone

 

AT2A1, Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

FRIH, Ferritin, heavy subunit

 

CAH1, Carbonic anhydrase 1

FRIM, Ferritin, middle subunit

 

CAHZ, Carbonic anhydrase

NUDT9, ADP-ribose pyrophosphatase, mitochondrial

 

CLDN28a, Claudin 28a

PLM, Phospholemman

 

CLDN32a, Claudin 32a

S4A11, Sodium bicarbonate transporter-like protein 11

 

CLDN38 D, Claudin 8d

SGK1, Serine/threonine-protein kinase Sgk1

 

CLDN3a, Claudin 3a

VDAC2, Voltage-dependent anion-selective channel protein 2

  1. Protein symbol and description of Swiss-Prot protein entries to which differentially expressed tags were annotated are shown. Criteria for inclusion each category were based on gene ontology annotation of Swiss-prot entries: category "Calcium-binding proteins"- genes annotated with molecular function "calcium ion binding", GO:0005509; "Transcription factors"- molecular function "transcription factor activity", GO:0003700; "Other regulators of transcription"- biological process "regulation of transcription", GO:0045449; "Components of signal transduction pathways/intracellular signaling"- genes annotated to biological process GO categories containing the words "signaling" or "signal transduction", and "Ion transporters/related to ion homeostasis or osmoregulation"- genes annotated to biological processes "ion transport", GO:0006811 or "ion homeostasis", GO:0050801. In the calcium binding protein (CaBP) category, * indicates proteins found in the CaBP database HTTP://structbio.vanderbilt.edu/cabp_database/; in the category components of signal transduction pathways, TF indicates transcription factors. For detailed information about tag sequences, counts, ratios of expression or clustering for each of these highlighted genes see Additional file 3.