Open Access

Erratum To: Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells

  • Hideki Ogino1, 2,
  • Tadashige Nozaki2,
  • Akemi Gunji2,
  • Miho Maeda1, 3,
  • Hiroshi Suzuki4,
  • Tsutomu Ohta5,
  • Yasufumi Murakami3,
  • Hitoshi Nakagama2,
  • Takashi Sugimura2 and
  • Mitsuko Masutani1, 2Email author
BMC Genomics20078:227

DOI: 10.1186/1471-2164-8-227

Received: 20 March 2007

Accepted: 10 July 2007

Published: 10 July 2007

The original article was published in BMC Genomics 2007 8:41

Background

Following the publication of the paper 'Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells' [1], we found an error in our data.

In the article, we used six replicates of microarray data of wild-type ES cells for comparison with the microarray data of Parp-1 knockout ES cells. We found that three replicate data were carelessly included in the data for wild-type ES cells. The comparison should have been carried out between three replicates for the Parp-1+/+ ES cell line, J1, and three replicates for two Parp-1-/- ES cell lines, 210–58 and 226–47, respectively.

Therefore, we re-analyzed the data in ES cells according to the same criteria. The consequences of this error are reflected in changes to our results although the conclusions we obtained in the study are not affected.

Corrected sentences in the Abstract

Here, we demonstrate that of the 9,640 genes analyzed, in Parp-1 -/- ES cells. 3.6% showed altered gene expression. Of these, 2.5% and 1.1% of the genes were down- or up-regulated by 2-fold or greater, respectively, compared with Parp-1+/+ ES cells (p < 0.05).

Corrected results in the text

Gene expression profile in Parp-1 -/- ES cells

A comparison of the basal gene expression profiles in Parp-1 -/- EScells to their wild-type (Parp-1 +/+ ) counterparts, is presented in Fig. 1A &1B (corrected) and Table 1 (corrected). We found the expression of (344/9,640) genes, namely 3.6%, was different by at least 2-fold between Parp-1 -/- and Parp-1 +/+ ES cells (p < 0.05) (Fig. 1B (corrected) and Table 1 (corrected)). Notably, a larger fraction of the genes, being 2.5%(238/9,640), was down-regulated, whereas only 1.1% (106/9,640) of the genes were up-regulated (see Table 1 (corrected)).
Table 1

Differential expression of genes between Parp-1+/+ and Parp-1-/- ES cells, livers, and EFs

 

No. of genes

  

Parp-1-/- <Parp-1+/+

Parp-1-/- > Parp-1+/+

p-value cut offa

Total

Total

2-fold or greater

Total

2-fold or greater

ES cellsc

     

Totalb

9,640

5,065

1,056

4,481

1,520

p < 0.05b

893

663

238

230

106

Liversd

     

Totalb

12,353

7,138

1,184

4,860

1,038

p < 0.05b

1,616

1,190

253

426

158

p < 0.01b

641

515

100

126

43

EFse

     

Total

12,357

5,042

707

7,317

501

p < 0.05

996

390

216

606

205

aAnalyzed by One-Way ANOVA (non-parametric test known as the Mann-Whitney U test)

bThese genes were presented in Fig. 1.

cParp-1+/+ ES cell clone, J1, and Parp-1-/- ES cell clones, 210–58 and 226–47, were used.

dTwo mice were used for each genotype.

eThree EFs obtained from three embryos were analyzed as triplicate experiments.

https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-8-227/MediaObjects/12864_2007_Article_940_Fig1_HTML.jpg
Figure 1

Effect of Parp-1 deficiency on gene expression. Gene expression data from microarray analyses are plotted for Parp-1 -/- versus wild-type (Parp-1 +/+ ) ES cell lines (A) & (B). Horizontal and vertical axes represent expression levels normalized for an individual gene. Each point represents normalized expression data for an individual gene. The genes that showed standard deviation greater than 2.0 in the normalized data of both genotypes (A) were excluded and gene lists were constructed with p < 0.05 (B). Fig. 1D–F in the original article [1] remains unchanged and is presented as (C) – (E), respectively.

We also made the heatmaps using the gene lists containing the 893 genes that showed a difference at p < 0.05 in ES cells (Fig. 2A (corrected)). Although we used independently isolated Parp-1 -/- ES cell clones, a clear and common alteration in the gene expression profile was observed (see Fig. 2A (corrected), and Tables 2 (corrected) and 3 (corrected)).
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-8-227/MediaObjects/12864_2007_Article_940_Fig2_HTML.jpg
Figure 2

Comparison of gene expression profiles among cell lines or cell types. Heatmaps of gene expression profiles in ES cells (A). We constructed the heatmaps using the gene lists containing the genes that showed a difference at p < 0.05 in ES cells. Each heatmap is constructed using GeneSpring GX ver. 7.3.1. Numbers of genes down-(C) or up-(D) regulated in common between Parp-1 -/- ES cells and livers. The numbers of the genes are indicated in Venn diagrams. These genes showed the difference with at least 2-fold between Parp-1 +/+ and Parp-1 -/- (p < 0.05). Fig. 2B in the original article [1] remains unchanged and is presented as (B). Fig. 2D & F in the original article [1] are removed and Fig. 2C & E were corrected in the original article [1] and are presented as (C) and (D).

Table 2

Genes down-regulated in Parp-1-/- ES cells

 

Fold changea)

   

Accession No.

W vs H

J1 vs 210–58

J1 vs 226–47

Symbol

Chromosome

Gene description

Cell cycle/cell proliferation/cell death

      

AW122355

3.2

5.2

2.3

Prkcbp1

2

Protein kinase C binding protein 1

AF067395

2.9

2.9

2.9

Bnip3l

14

BCL2/adenovirus E1B 19 kDa-interacting protein

AI842277

2.7

2.3

3.2

Igfbp3

11

Insulin-like growth factor binding protein 3

U95826

2.2

2.5

1.9

Ccng2

5

Cyclin G2

Cell structure/cell adhesion

      

U16741

4.1

6.3

3.1

Capza2

6

Capping protein (actin filament) muscle Z-line, alpha 2

AI132380

3.6

3.1

4.3

Fndc3a

14

Fibronectin type III domain containing 3a

AI505453

2.9

2.5

3.4

Myh9

15

Myosin, heavy polypeptide 9, non-muscle

AW208938

2.4

3.2

2.0

Pkp2

16

Plakophilin 2

M76124

2.4

2.2

2.6

Tacstd1

17

Tumor-associated calcium signal transducer 1

Metabolism

      

U73820

5.5

5.2

5.8

Galnt1

18

Polypeptide GalNAc transferase-T1 (ppGaNTase-T1)

AI841270

3.4

2.4

6.4

Gstm1

3

Glutathione S-transferase, mu1

AV308550

2.6

4.1

1.9

Piga

x

Phosphatidylinositol glycan, class A

AI851912

2.3

2.2

2.5

Rps27

3

Ribosomal protein S27

AI852144

2.1

2.9

1.7

Pbef-pending

12

Pre-B-cell colony-enhancing factor

U65986

2.1

1.9

2.5

Anxa11

14

Annexin A11

D50264

2.1

1.4

4.1

Pigf

17

Phosphatidylinositol glycan, class F

AF031486

2.0

2.0

2.0

Sms

x

Spermidine synthase

AI845882

2.0

2.5

1.7

Acyp1

12

Acylphosphatase1, erythrocyte (common) type

Protein biosynthesis/degradation

      

AI852581

3.0

3.0

3.1

Ide

19

Insulin degradating enzyme

AI414051

3.0

1.8

9.1

Usp24

4

Ubiquitin specific protease 24

AW121012

2.9

2.8

3.0

Rnf19

15

Ring finger protein 19

X92665

2.9

2.5

3.4

Ube2e1

14

Ubiquitin-conjugating enzyme UbcM3

AW048882

2.2

2.8

1.8

Iars

13

Isoleucine-tRNA synthetase

AA867340

2.2

1.9

2.6

Psme4

11

Proteasome (prosome, macropain) activator subunit

AB024427

2.2

2.3

2.1

Rnf11

4

Ring finger protein 11

Signaling

      

AI846023

4.6

2.8

13.1

Arl7

1

ADP-ribosylation factor-like 7

AA260005

2.8

2.7

2.8

Pawr

10

PPKC, apoptosis, WT1, regulator

AI317205

2.6

2.4

2.7

Map3k1

13

Mitogen activated protein kinase kinase kinase 1

AF035644

2.3

2.0

2.7

Ptp4a2

4

Protein tyrosine phosphatase 4a2

M21019

2.3

1.9

2.9

Rras

7

Harvey rat sarcoma oncogene, subgroup R

AI194248

2.2

2.5

1.9

Csnk2a1

2

Casein kinase II, alpha 1 polypeptide

AI854006

2.0

2.0

2.1

Set

2

SET translocation

D83921

2.0

1.9

2.1

Ebaf

1

Endometrial bleeding associated factor

Transcription/replication

      

X14206

9.9

8.4

11.9

Adprt1

1

Poly(ADP-ribose) polymerase 1

M99167

3.0

6.2

2.0

Hnrpa1

15

Heterogeneous nuclear ribonucleoprotein A1

AW107922

2.8

3.7

2.2

Sox11

12

SRY-box containing gene 11

AI849135

2.5

2.5

2.5

Foxo3a

10

Forkhead box 03a

Y07836

2.5

2.3

2.8

Bhlhb2

6

Basic-helix-loop-helix domain containing, class B2

X74760

2.5

2.3

2.7

Notch3

17

Notch gene homolog 3, (Drosophila)

AI447783

2.1

2.4

1.9

Helb

10

Helicase (DNA) B

X94694

2.1

2.7

1.7

Tcfap2c

2

Transcription factor AP-2, gamma

AF077861

2.1

2.2

2.1

Id2

12

Inhibitor of DNA binding 2

AI605405

2.0

1.9

2.3

Phf13

4

PHD finger protein 13

D78382

2.0

1.7

2.6

Tob1

11

Transducer of ErbB2.1

Transport

      

AV356315

4.1

5.5

3.3

Lman1

18

Lectin, mannose-binding, 1

AV298789

2.9

2.6

3.2

Ranbp5

14

Ran binding protein 5

D88315

2.2

2.2

2.2

Hiat1

3

Hippocampus abundant gene transcript 1

Unknown

      

AI845617

3.5

3.5

3.4

2610019A05Rik

11

Hypothetical protein

AI852287

3.2

3.3

3.2

Ankrd28

14

Ankyrin repeat domain 28

AI836771

3.0

2.8

3.3

2900008M13Rik

15

Unknown EST

AA684456

2.9

2.1

4.5

2310015N07Rik

7

Hypothetical protein

AI848435

2.8

1.9

4.8

C78339

13

Unknown EST

AW123157

2.8

2.5

3.1

1700051E09Rik

11

Hypothetical protein

AW124843

2.6

3.1

2.3

C85108

4

Unknown EST

AA710439

2.6

2.0

3.6

6230421P05Rik

16

Unknown EST

AI853444

2.5

1.8

3.9

2610042L04Rik

14

Hypothetical protein

AI853444

2.2

2.1

2.3

2610042L04Rik

14

Hypothetical protein

AW121353

2.1

1.6

3.1

Lrrc8

2

Luecine rich repeat containing 8

AI037493

2.1

1.5

3.4

Tbc1d15

10

TBC1 domain family, member 15

AI461803

2.1

2.2

1.9

1300006C19Rik

9

Hypothetical protein

AW049969

2.0

2.0

2.1

C330005L02Rik

9

Hypothetical protein

AI847483

2.0

2.0

2.0

Tmem41b

7

Transmembrane protein 41B

a)W, wild-type cells (J1); H, Parp-1-/- ES cells (210–58 and 226–47).

Table 3

Genes up-regulated in Parp-1-/- ES cells

 

Fold changea)

   

Accession No.

H vs W

210–58 vs J1

226–47 vs J1

Symbol

Chromosome

Gene description

Cell cycle/cell proliferation/cell death

      

X58196

3.1

3.3

2.9

H19

7

H19 non-coding RNA

AI842665

3.0

3.1

2.8

Tax1bp3

11

Human T-cell leukemia virus type I binding protein 3

Cell structure/cell adhesion

      

X04017

2.3

2.3

2.3

Sparc

11

Cysteine-rich glycoprotein SPARC

M26071

2.1

2.5

1.8

F3

3

Coagulation factor III

M91236

2.1

2.1

2.1

Gjb5

4

Gap junction membrane channel protein beta 5

Immune response

      

U13705

2.3

2.1

2.4

Gpx3

11

Glutathione peroxidase 3

Metabolism

      

AW120625

2.3

1.9

2.7

Pgd

4

Phosphogluconate dehydrogenase

M64782

2.2

1.9

2.5

Folr1

7

Folate-binding protein 1 (FBP1)

X97755

2.0

2.1

2.0

Ebp

x

Phenylalkylamine Ca2+ antagonist (emopamil) binding protein

Protein biosynthesis/degradation

      

W71352

3.9

4.2

3.6

Bag2

1

Bcl2-associated athanogene 2

AI844175

3.4

3.4

3.4

Mrps11

7

Mitochondrial ribosomal protein S11

U16163

2.9

2.9

2.8

P4ha2

11

Prolyl 4-hydroxylase alpha(II)-subunit

D00622

2.5

2.0

3.0

Lrpap1

5

Low density lipoprotein receptor related protein, associated protein 1

X60676

2.3

2.4

2.2

Serpinh1

7

HSP47

AW124432

2.1

1.8

2.5

Mrpl12

11

Mitochondrial ribosomal protein L12

AI839392

2.0

2.0

2.1

Aars

8

Alanyl-tRNA syntase

Transcription/replication

      

D49473

3.4

3.0

3.7

Sox17

1

SRY-box containing gene 17

U51335

2.5

2.5

2.6

Gata6

18

GATA-binding protein 6

U79962

2.4

2.1

2.6

Tarbp2

15

TAR (HIV) RNA binding protein 2

D49473

2.1

1.9

2.3

Sox17

1

SRY-box containing gene 17

Transport

      

D14077

2.2

2.1

2.3

Clu

14

Clusterin

Others

      

M34603

2.6

2.3

3.0

Prg

10

Proteoglycan core protein

AA793009

2.3

2.0

2.7

Tex19

11

Testis expressed gene 19

Unknown

      

AI846553

3.2

3.0

3.3

1110020C13Rik

15

Hypothetical protein

AI845664

2.1

2.0

2.2

Grwd

7

Glutamate-rich WD repeat containing 1

a)H, Parp-1-/- ES cells (210–58 and 226–47); W, wild-type cells (J1).

We further selected the genes that showed relatively high expression levels (the "Flag value" in GeneSpring ver. 6.1 of the genes should be either "Present" (high level of expression) or "Marginal" (moderate level of expression) in all replicates of the genotype within the 893 genes that showed a difference at p < 0.05, see Table 1 (corrected)). Among the 85 genes selected by this analysis, there were 61 genes, obviously including the Parp-1 (Adprt1) gene itself, that were down-regulated and 24 genes up-regulated, as listed in Tables 2 (corrected) and 3 (corrected).

Gene expression profile of the livers and EF cells

In the livers, 3.3% (411/12,353) of genes showed a significant difference in expression level (p < 0.05) between the Parp-1 genotypes. In the livers of Parp-1 -/- mice, 2.0% (253/12,353) of the genes were down-regulated and 1.3% (158/12,353) of the genes were up-regulated (p < 0.05). Similar to Parp-1 -/- ES cells, a higher percentage of the genes, 62% (253/411), were down-regulated and the remaining 38% were up-regulated (Fig. 1C–E in the original article [1], and Table 1 (corrected)). The expression of representative marker genes of the liver, including albumin (Alb1) and phosphoenolpyruvate carboxykinase (Pepck), was similarly high in both Parp-1 genotypes.

The heatmaps were constructed using the gene lists containing the 641 genes that showed a difference at p < 0.01 in livers (Fig. 2B). Parp-1 deficiency commonly altered gene expression profiles in the livers of two mice analyzed (Fig. 2B, and Table 4 in the original article [1]).

Comparison of the profiles among different cell types

We compared gene expression profiles between Parp-1-/- ES cells and the livers. There were no genes commonly up- or down-regulated as summarized in Tables 2 (corrected), 3 (corrected), and 4 in the original article [1], namely in the genes showing relatively high expression levels selected by Flag values, although we observed that 7 genes, including Eif2s2 (eukaryotic translation initiation factor 2 subunit 2 beta), Parp-1, and 1 gene Crygs (crystallin gamma S), were commonly down- and up-regulated in the ES cells and livers (p < 0.05), respectively (Fig. 2C (corrected) &2D (corrected)).

Corrected methods in the text

Data analysis

Data analysis was performed with the GeneSpring® software ver. 6.1 and ver. 7.3.1 (the latest version). For statistical analyses, the fluorescence intensity (raw signal) was normalized to the 50th percentile reading per chip, and then normalized to the median reading per gene. We performed the non-parametric tests with the cross-gene error model being inactive. In the case of Parp-1-/- ES cells, 6 replicates consisting of triplicate microarray results from two Parp-1-/- ES cell lines were used. We used the triplicate microarray results from the Parp-1+/+ ES cell line, J1. We excluded genes that showed a standard deviation greater than 2.0 in the normalized data of both genotypes, and we started analysis with 9,640 genes and ESTs for ES cells (Table 1 (corrected)). We constructed gene lists only with the genes that showed statistical differences (p < 0.05) and 2-fold or greater differences in normalized expression levels between Parp-1 genotypes. To construct heatmaps, we used GeneSpring® GX ver. 7.3.1 (the latest version).

We regret that this error occurred in the phase of generating the data set in our paper may have caused any inconvenience. In the process of making these corrections, the microarray data were submitted to the gene expression database CIBEX [2] with the following accession number: CBX22.

Notes

Declarations

Authors’ Affiliations

(1)
ADP-ribosylation in Oncology Project, National Cancer Center Research Institute
(2)
Biochemistry Division, National Cancer Center Research Institute
(3)
Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science
(4)
Chugai Pharmaceutical Co. Ltd.
(5)
Center for Medical Genomics, National Cancer Center Research Institute

References

  1. Ogino H, Nozaki T, Gunji A, Maeda M, Suzuki H, Ohta T, Murakami Y, Nakagama H, Sugimura T, Masutani M: Loss of Parp-1 affects gene expression profile in a genome-wide manner in ES cells and liver cells. BMC Genomics. 2007, 8: 41-10.1186/1471-2164-8-41.PubMed CentralPubMedView ArticleGoogle Scholar
  2. Center for Information Biology Gene Expression Database. [http://cibex.nig.ac.jp]

Copyright

© Ogino et al; licensee BioMed Central Ltd. 2007

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.