How to use the BREReA package to remove background, register the 1D expression patterns of segmentation genes, and construct reference data

To uncover the transcriptomic mechanism of lignin accumulation caused by boron deficiency (BD), Nanlin895 (Populus × euramericana “Nanlin895”) was subjected to control (CK, 0.25 mg·L−1) and BD (0 mg·L−1) treatments for 3 days. RNA-Seq was carried out to survey the expression patterns of the lignin-regulated biosynthetic genes in response to BD. The results showed that 5946 genes were identified as differentially expressed genes (DEGs), 2968 (44.2%) of which were upregulated and 3318 (55.8%) of which were downregulated in response to BD. Among them, the expression of lignin monomer biosynthetic (PAL, CCR, CAD, COMT, F5H, PER/LAC) and modulated genes, for example, transcription factors (MYBs) and hormone signal regulating genes (GIDs, histidine kinase 1, coronatine-insensitive protein 1), were upregulated, and some hormone signal regulating genes, such as AUXs and BR-related (sterol methyltransferases), were downregulated under BD treatment. There are also some genes that were screened as candidates for an association with wood formation, which will be used for the further analysis of the function of lignin formation. These results provide an important theoretical basis and reference data in plant for further research on the mechanism of lignin accumulation under BD.

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Fast redundant dyadic wavelet transform in application to spatial registration of the expression patterns of Drosophila segmentation genes

Proceedings 15th International Conference on Pattern Recognition. ICPR-2000 ◽

10.1109/icpr.2000.903583 ◽

2002 ◽

Author(s):

K. Kozlov ◽

E. Myasnikova ◽

M. Samsonova ◽

J. Reinitz ◽

D. Kosman

Keyword(s):

Wavelet Transform ◽

Expression Patterns ◽

Segmentation Genes ◽

Dyadic Wavelet ◽

Spatial Registration ◽

Dyadic Wavelet Transform

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Expression patterns of hairy, even-skipped, and runt in the spider Cupiennius salei imply that these genes were segmentation genes in a basal arthropod

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.97.9.4515 ◽

2000 ◽

Vol 97 (9) ◽

pp. 4515-4519 ◽

Cited By ~ 86

Author(s):

W. G. M. Damen ◽

M. Weller ◽

D. Tautz

Keyword(s):

Expression Patterns ◽

Cupiennius Salei ◽

Segmentation Genes ◽

Spider Cupiennius Salei

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Registration of the expression patterns of Drosophila segmentation genes by two independent methods

Bioinformatics ◽

10.1093/bioinformatics/17.1.3 ◽

2001 ◽

Vol 17 (1) ◽

pp. 3-12 ◽

Cited By ~ 78

Author(s):

E. Myasnikova ◽

A. Samsonova ◽

K. Kozlov ◽

M. Samsonova ◽

J. Reinitz

Keyword(s):

Expression Patterns ◽

Segmentation Genes

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Positive and negative control of the Antennapediapromoter P2

Development ◽

10.1242/dev.113.supplement_1.177 ◽

1991 ◽

Vol 113 (Supplement_1) ◽

pp. 177-185 ◽

Cited By ~ 1

Author(s):

George R. Riley ◽

Erik M. Jorgensen ◽

Robert K. Baker ◽

Richard L. Garber

Keyword(s):

Expression Patterns ◽

Negative Control ◽

Segmentation Genes ◽

Active Gene ◽

Inhibitory Drug

To understand the nature of the regulatory signals impinging on the second promoter of the Antennapedia gene (Antp P2), analysis of its expression in mutants and in inhibitory drug injected embryos has been carried out. The maternally-active gene osk is identified as one of two general repressors of P2 which prevent Antp transcription until division cycle 14. Products of the zygotically-active segmentation genes ftz, hb, Kr, gt and kni then act as activators or repressors of Antp P2 in a combinatorial fashion. The timing of these events, and their positive versus negative nature, is critical for generating the expression patterns normal for Antp.

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Clausal Density Between Ages 4 and 9 Years for the Edmonton Narrative Norms Instrument: Reference Data and Psychometric Properties

Language Speech and Hearing Services in Schools ◽

10.1044/2020_lshss-20-00043 ◽

2020 ◽

pp. 1-15

Author(s):

Ling-Yu Guo ◽

Phyllis Schneider ◽

William Harrison

Keyword(s):

Diagnostic Accuracy ◽

Psychometric Properties ◽

Language Impairment ◽

Reference Data ◽

Reliability And Validity ◽

Correlation Coefficients ◽

Criterion Validity ◽

Likelihood Ratios ◽

Generation Task ◽

Sensitivity Specificity

Purpose This study provided reference data and examined psychometric properties for clausal density (CD; i.e., number of clauses per utterance) in children between ages 4 and 9 years from the database of the Edmonton Narrative Norms Instrument (ENNI). Method Participants in the ENNI database included 300 children with typical language (TL) and 77 children with language impairment (LI) between the ages of 4;0 (years;months) and 9;11. Narrative samples were collected using a story generation task, in which children were asked to tell stories based on six picture sequences. CD was computed from the narrative samples. The split-half reliability, concurrent criterion validity, and diagnostic accuracy were evaluated for CD by age. Results CD scores increased significantly between ages 4 and 9 years in children with TL and those with LI. Children with TL produced higher CD scores than those with LI at each age level. In addition, the correlation coefficients for the split-half reliability and concurrent criterion validity of CD scores were all significant at each age level, with the magnitude ranging from small to large. The diagnostic accuracy of CD scores, as revealed by sensitivity, specificity, and likelihood ratios, was poor. Conclusions The finding on diagnostic accuracy did not support the use of CD for identifying children with LI between ages 4 and 9 years. However, given the attested reliability and validity for CD, reference data of CD from the ENNI database can be used for evaluating children's difficulties with complex syntax and monitoring their change over time. Supplemental Material https://doi.org/10.23641/asha.13172129

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