#158. Replace entities names in the dataset with existing ones

scripts/expression_change_human_mrna/08-09-2023-update-items-human-mrna.csv

@@ -17,8 +17,8 @@ HMGB2,10.1007/s11357-018-0015-1,human,n/a,all,209.0%,,plasma,20,70,20,70,24,84,y
 HMGB2,10.1007/s11357-018-0015-1,human,n/a,all,292.0%,,plasma,20,90,20,90,24,100,years,increased gene expression,4,108,Pearson correlation,protein,ELISA,"The data for 20-24 vs. 90-100 years old. Circulating levels of HMGB2 in human plasma were investigated. Control - young donors 20-24 years old (n=4). The old donors were a cohort of 108 people aged 70 to 100 years (n=108). Protein concentrations were measured by the ELISA kit from Lifespan Biosciences (LS-F11643-1). HMGB2 levels increased with age (R2 value=0.0826, Pearson correlation=0.546). Absolute levels of HMGB2 ranged from 0.4 to 7.9 ng/ml.",n/a
 FOXO1,10.1007/s10522-007-9114-6,rat,F344,male,66.0%,<0.001,kidney,n/a,n/a,6,24,n/a,n/a,months,reduced protein activity,3,3,"ANOVA, Fisher's test",protein,EMSA,The EMSA method was used to compare nuclear FOXO binding activities in kidney nuclear protein from rats. FOXO activity was decreased with age. The caloric restriction protects from age-related FOXO binding activity decreasing.,n/a
 FOS,10.1002/jnr.10428,rat,F344,all,32.0%,<0.02,hippocampus,n/a,n/a,3,30,n/a,n/a,months,reduced protein activity,4,4,two-tailed t test,protein,EMSA,"Measurements of AP-1 binding activity by EMSA over time after hyperoxia also showed significant increases in AP-1 DNA binding activity after 24 hr of hyperoxia. When aged animals were also challenged with a hyperoxia insult, there were no significant increases in AP-1 binding activity",n/a
-LAIR1,10.1002/eji.200636678,human,n/a,all,30.0%,<0.001,CD4+ T lymphocytes,"0,4",22,n/a,n/a,1,68,years,decreased gene expression,16,25,Mann-Whitney test,protein,flow cytometry,"110 healthy humans of varios age participated in the stuly. The Lair1 gene expression decreases in the CD4 T lymphocytes with age, significant diferences were found between the ages 0 and >20 years. At the same time, these differences were caused by the reduction of the naive T-cells and not by the change in the Lair1 expression in the any of the T-cell subpopulations. The Lair1 expression was consistently higher in the naive T-cells, than in the memory T-cells and do not shows any significant changes with time in the any T-cell subpopulation.",n/a
-LAIR1,10.1002/eji.200636678,human,n/a,all,47.0%,0.002,CD8+ T lymphocytes,"0,4",22,n/a,n/a,1,68,years,decreased gene expression,16,25,Mann-Whitney test,protein,flow cytometry,"110 healthy humans of varios age participated in the stuly. The Lair1 gene expression decreases in the CD8 T lymphocytes with age, significant diferences were found between the ages 0 and >20 years. At the same time, these differences were caused by the reduction of the naive T-cells and not by the change in Lair1 expression in the any of the T-cell subpopulations. The Lair1 expression was consistently higher in the naive T-cells, than in the memory T-cells and do not shows any significant changes with time in the any T-cell subpopulation.",n/a
+LAIR1,10.1002/eji.200636678,human,n/a,all,30.0%,<0.001,CD4+ T cells,"0,4",22,n/a,n/a,1,68,years,decreased gene expression,16,25,Mann-Whitney test,protein,flow cytometry,"110 healthy humans of varios age participated in the stuly. The Lair1 gene expression decreases in the CD4 T lymphocytes with age, significant diferences were found between the ages 0 and >20 years. At the same time, these differences were caused by the reduction of the naive T-cells and not by the change in the Lair1 expression in the any of the T-cell subpopulations. The Lair1 expression was consistently higher in the naive T-cells, than in the memory T-cells and do not shows any significant changes with time in the any T-cell subpopulation.",n/a
+LAIR1,10.1002/eji.200636678,human,n/a,all,47.0%,0.002,CD8+ T cells,"0,4",22,n/a,n/a,1,68,years,decreased gene expression,16,25,Mann-Whitney test,protein,flow cytometry,"110 healthy humans of varios age participated in the stuly. The Lair1 gene expression decreases in the CD8 T lymphocytes with age, significant diferences were found between the ages 0 and >20 years. At the same time, these differences were caused by the reduction of the naive T-cells and not by the change in Lair1 expression in the any of the T-cell subpopulations. The Lair1 expression was consistently higher in the naive T-cells, than in the memory T-cells and do not shows any significant changes with time in the any T-cell subpopulation.",n/a
 PDGFRA,10.1002/oby.21727,mouse,C57BL/6J,male,30.6%,<0.05,inguinal white adipose tissue,n/a,n/a,4,20,n/a,n/a,months,decreased gene expression,7,7,n/a,number of cells expressing the gene,flow cytometry,Flow cytometry.,n/a
 IFNG,10.1006/clim.2000.4894,human,n/a,all,n/a,<0.01,T-cells,n/a,17,n/a,n/a,n/a,62,years,increased gene expression,n/a,50,Spearman coefficient,protein,flow cytometry,The production of IFN-γ in CD8+high T cells is directly correlated with age. 50 individuals were investigated.,n/a
 NGB,10.1007/s10072-017-3168-2,mouse,B6CBAF1/J,male,50.0%,<0.05,striatum,n/a,n/a,7,13,n/a,n/a,months,decreased gene expression,4,4,"ANOVA, Tukey's test",protein,immunohistochemistry,n/a,n/a
@@ -93,15 +93,15 @@ FOLR2,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.00028212,skin,n/a,39,n/a,n
 GPX4,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.000609809,skin,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Gene expression of GPX4 decreases with age.,n/a
 MTR,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.000118645,skin,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,"Using a linear mixed model, differential expression with age was identified in MTR in skin. Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. The linear mixed model was used to examine gene expression variability by age.",n/a
 NIPBL,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.001537566,skin,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,A linear mixed model was used to examine gene expression variability by age in samples from photoprotected infra-umbilical skin of female twins.,n/a
-RET,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.004114123,fat,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,"Using a linear mixed model, differential expression with age was identified in RET in the adipose tissue. Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. Subcutaneous adipose tissue was dissected from the biopsy site. The linear mixed model was used to examine gene expression variability by age.",n/a
-SMOC1,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.002063429,fat,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. Subcutaneous adipose tissue was dissected from the biopsy site. The linear mixed model was used to examine gene expression variability by age.,n/a
+RET,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.004114123,adipose tissue,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,"Using a linear mixed model, differential expression with age was identified in RET in the adipose tissue. Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. Subcutaneous adipose tissue was dissected from the biopsy site. The linear mixed model was used to examine gene expression variability by age.",n/a
+SMOC1,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.002063429,adipose tissue,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. Subcutaneous adipose tissue was dissected from the biopsy site. The linear mixed model was used to examine gene expression variability by age.,n/a
 SMOC2,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.00305753,skin,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. The linear mixed model was used to examine gene expression variability by age.,n/a
 TRPV1,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.007947182,skin,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Differential expression with age was identified in TRPV1 in skin. Biopsies were taken from relatively photo-protected infra-umbilical skin of female twins. The linear mixed model was used to examine gene expression variability by age.,n/a
 UCP2,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.000403425,skin,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Gene expression of UCP2 decreases with age in а female skin.,n/a
 AHSP,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,2.56e-05,skin,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,Expression of the AHSP gene decreases with age in the skin of the abdomen. A total of 856 female twins at the age from 39 to 85 years old were investigated.,n/a
 ELMO1,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.008517023,skin,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,ELMO1 is downregulated in aged human skin as revealed by microarray analysis and logistic regression model.,n/a
 DLK2,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,5.31e-08,skin,n/a,39,n/a,n/a,n/a,85,years,increased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,DLK2 is upregulated in aged human skin as revealed by microarray analysis and logistic regression model.,n/a
-BCL6,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,9.15e-06,fat,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,BCL6 is downregulated in aged human adipose tissue as revealed by microarray analysis and logistic regression model.,n/a
+BCL6,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,9.15e-06,adipose tissue,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,BCL6 is downregulated in aged human adipose tissue as revealed by microarray analysis and logistic regression model.,n/a
 PPM1H,10.1186/gb-2013-14-7-r75,human,n/a,female,n/a,0.007007389,skin,n/a,39,n/a,n/a,n/a,85,years,decreased gene expression,n/a,856,"chi-square, Benjamini-Hochberg correction for multiple testing",mRNA,microarray,"Punch biopsies (8mm) were taken from photoprotected infra-umbilical skin of female twins. A linear mixed model was used to examine gene expression variability by age and confounding factors including as fixed effect batch and RNA concentration (only in skin samples), and as random effects family relationship and zygosity. Information about gene is in additional online files.",n/a
 IKBKB,10.1007/s10495-013-0806-x,rhesus monkey,Macaca mulatta,all,125.0%,0.0034,oral mucosa,3,18,n/a,n/a,7,23,years,increased gene expression,5,5,linear regression,mRNA,"microarray, qPCR",n/a,n/a
 IKBKB,10.1007/s10495-013-0806-x,rhesus monkey,Macaca mulatta,all,50.0%,0.0034,oral mucosa,3,12,n/a,n/a,7,16,years,increased gene expression,5,8,linear regression,mRNA,"microarray, qPCR",n/a,n/a
@@ -291,8 +291,8 @@ COL4A6,10.1111/j.1523-1755.2005.00668.x,dog,n/a,male,335.0%,,testis,n/a,n/a,60,9
 COL4A6,10.1111/j.1523-1755.2005.00668.x,dog,n/a,male,10.0%,,testis,n/a,n/a,60,210,n/a,n/a,days,decreased gene expression,n/a,n/a,n/a,mRNA,northern blot,n/a,n/a
 GCLC,10.1002/jcp.20496,rat,F344,male,30.0%,0.01,aorta,n/a,n/a,6,24,n/a,n/a,months,increased gene expression,4,4,Student t-test,mRNA,northern blot,"GCLC mRNA levels were higher in vascular smooth muscle cells from old rats compared to young, a pattern consistent with its protein levels.",n/a
 TGM2,10.1007/s00726-016-2295-z,rat,F344,male,229.0%,0.004,heart,n/a,n/a,6,18,n/a,n/a,months,increased protein activity,6,6,"ANOVA, Tukey's test",n/a,protein acivity assay,The transamidation activity of TGM2 was assessed.,27438265
-CSF2,10.1007/s11033-012-2219-2,mouse,C57BL/6,male,1500.0%,<0.05,CD4+ T lymphocytes,n/a,n/a,2,16,n/a,n/a,weeks,increased gene expression,3,3,ANOVA,mRNA,qPCR,"CD4+ T cells were isolated from the spleens of C57BL/6 mice (weeks 2 and 16). Total RNA was obtained from unstimulated CD4+ T cells. In young mice (2 weeks old) a very low level of Csf2 mRNA expression was obtained, while in old mice, a significantly increased level of Csf2 expression was observed — approximately 15 times higher.",n/a
-NFKB1,10.1007/s11033-012-2219-2,mouse,C57BL/6,male,446.0%,<0.05,CD4+ T lymphocytes,n/a,n/a,2,16,n/a,n/a,weeks,increased gene expression,3,3,ANOVA,mRNA,qPCR,"Populations of CD4+ T cells from the spleen were obtained. The method is real-time RT-PCR, the data are normalized to the UBC gene and presented as the average of three independent experiments. An extraordinary expression increase was shown - by 5.46 times.",n/a
+CSF2,10.1007/s11033-012-2219-2,mouse,C57BL/6,male,1500.0%,<0.05,CD4+ T cells,n/a,n/a,2,16,n/a,n/a,weeks,increased gene expression,3,3,ANOVA,mRNA,qPCR,"CD4+ T cells were isolated from the spleens of C57BL/6 mice (weeks 2 and 16). Total RNA was obtained from unstimulated CD4+ T cells. In young mice (2 weeks old) a very low level of Csf2 mRNA expression was obtained, while in old mice, a significantly increased level of Csf2 expression was observed — approximately 15 times higher.",n/a
+NFKB1,10.1007/s11033-012-2219-2,mouse,C57BL/6,male,446.0%,<0.05,CD4+ T cells,n/a,n/a,2,16,n/a,n/a,weeks,increased gene expression,3,3,ANOVA,mRNA,qPCR,"Populations of CD4+ T cells from the spleen were obtained. The method is real-time RT-PCR, the data are normalized to the UBC gene and presented as the average of three independent experiments. An extraordinary expression increase was shown - by 5.46 times.",n/a
 NFKB2,10.1007/s11033-012-2219-2,mouse,C57BL/6,male,389.5%,<0.05,CD4+ T cells,n/a,n/a,2,16,n/a,n/a,weeks,increased gene expression,3,3,ANOVA,mRNA,qPCR,"Populations of CD4+ T cells from the spleen were obtained. The method is real-time RT-PCR, the data are normalized to the UBC gene and presented as the average of three independent experiments. An extraordinary expression increase was shown — by 4.89 times.",n/a
 EGR1,10.1002/hipo.22583,rat,F344,male,55.0%,0.295,hippocampal dentate gyrus,9,24,n/a,n/a,12,32,months,decreased gene expression,3,3,"ANOVA, Bonferroni’s post hoc",mRNA,qPCR,"It was shown an age-related reduction in the transcription of Egr1 in the dentate gyrus following spatial behavior, whereas in the area CA1, Egr1 is reduced at rest, but its transcription can be effectively driven by spatial behavior to levels equivalent to those observed in adult animals. One mechanism possibly contributing to these aging-related changes is an age-associated, CpG site-specific change in methylation in DNA associated with the promoter region of the Egr1 gene. Complex transcriptional and epigenetic changes in the hippocampus significantly contribute to brain and cognitive aging. mRNA was measured by real time RT-PCR .",n/a
 HTRA2,10.1007/s11357-012-9406-x,rat,Sprague Dawley,male,300.0%,<0.01,heart,6,20,7,22,8,24,months,increased gene expression,10,10,"ANOVA, Bonferroni’s post hoc",mRNA,qPCR,n/a,n/a
@@ -565,7 +565,7 @@ ACOX1,10.1007/s10072-013-1509-3,rat,Sprague Dawley,male,32.0%,<0.05,liver,n/a,n/
 PPARA,10.1007/s11064-005-8341-y,rat,F344,female,48.0%,<0.05,spleen,n/a,n/a,3,18,n/a,n/a,months,decreased gene expression,4-6,4-6,Student t-test,protein,western blot,Method — Western Blot.,n/a
 NRIP1,10.1007/s11357-008-9062-3,mouse,AKR,male,60.0%,<0.05,liver,20,60,25,65,30,70,weeks,decreased gene expression,n/a,n/a,Student t-test,protein,western blot,n/a,n/a
 NRIP1,10.1007/s11357-008-9062-3,mouse,AKR,male,58.0%,<0.05,kidney,20,60,25,65,30,70,weeks,decreased gene expression,n/a,n/a,Student t-test,protein,western blot,n/a,n/a
-NRIP1,10.1007/s11357-008-9062-3,mouse,AKR,male,325.0%,<0.05,fat,20,60,25,65,30,70,weeks,increased gene expression,n/a,n/a,Student t-test,protein,western blot,n/a,n/a
+NRIP1,10.1007/s11357-008-9062-3,mouse,AKR,male,325.0%,<0.05,adipose tissue,20,60,25,65,30,70,weeks,increased gene expression,n/a,n/a,Student t-test,protein,western blot,n/a,n/a
 NGF,10.1007/s11357-011-9262-0,rat,Sprague Dawley,male,65.0%,<0.05,left ventricle,"0,4",6,0.5,7,"0,6",8,weeks,decreased gene expression,3,3,Student t-test,protein,western blot,n/a,n/a
 NGF,10.1007/s11357-011-9262-0,rat,Sprague Dawley,male,150.0%,<0.05,left ventricle,6,80,7,88,8,96,weeks,increased gene expression,3,3,Student t-test,protein,western blot,n/a,n/a
 NGF,10.1007/s11357-011-9262-0,rat,Sprague Dawley,male,50.0%,<0.05,left atrium,"0,4",6,0.5,7,"0,6",8,weeks,increased gene expression,3,3,Student t-test,protein,western blot,n/a,n/a