MtlD refers to a gene that encodes for the enzyme mannitol-1-phosphate dehydrogenase. This enzyme is involved in the metabolism of mannitol, a sugar alcohol that serves as a source of carbon and energy for certain microorganisms. Mannitol-1-phosphate dehydrogenase catalyzes the conversion of mannitol-1-phosphate to fructose-6-phosphate, which can then be further processed in the glycolysis pathway to generate energy (ATP).

The MtlD gene is present in a variety of bacteria and some fungi, where mannitol metabolism plays a role in their growth and survival. In some plant-associated bacteria, mannitol may be utilized as a compatible solute to help these bacteria cope with osmotic stress in their environment. Additionally, in some pathogenic bacteria, the ability to metabolize mannitol may provide a competitive advantage during infection or colonization of host tissues.

Understanding the function and regulation of MtlD and its corresponding enzyme is important for the study of bacterial metabolism, stress adaptation, and potential applications in biotechnology or as a target for developing antimicrobial strategies.

MtlD是指编码甘露醇-1-磷酸脱氢酶的基因。这种酶参与甘露醇的代谢，甘露醇是一种糖醇，为某些微生物提供碳源和能量。甘露醇-1-磷酸脱氢酶催化甘露醇-1-磷酸转化为果糖-6-磷酸，然后在糖酵解途径中进一步处理以产生能量（ATP）。

MtlD基因存在于多种细菌和一些真菌中，在它们的生长和生存中，甘露醇代谢起着重要作用。在一些与植物相关的细菌中，甘露醇可能被用作兼容溶质，帮助这些细菌应对环境中的渗透压应激。此外，在一些致病细菌中，代谢甘露醇的能力可能在感染或定殖宿主组织过程中提供竞争优势。

了解MtlD及其相应酶的功能和调控对于研究细菌代谢、抗压适应以及在生物技术中的潜在应用或作为开发抗微生物策略的靶标具有重要意义。

acrA和acrB基因编码的AcrA和AcrB蛋白质是AcrAB-TolC泵的两个组成部分。AcrA是一种膜融合蛋白，位于AcrB和TolC之间，起到连接的作用。AcrB是一种跨膜效应器蛋白，能够识别各种不同类型的有毒化合物并驱动其从细胞内排出。TolC是一种外膜通道蛋白，负责将底物从细胞内排到细胞外。这三个蛋白质共同组成了AcrAB-TolC泵，使细菌能够有效地排出各种有毒化合物。

除了在细菌的抗生素耐药性中起着重要的作用之外，acrA和acrB基因在细菌的生长和代谢中也发挥着重要的作用。例如，在某些细菌中，AcrAB-TolC泵可能参与细胞外分泌、细胞表面性状的调控、生物膜的合成等重要的生理过程。

在临床实践中，对于抗生素治疗失效的细菌感染，常常是由于这些细菌已经发展出了对多种抗生素的耐药性。因此，对acrA和acrB基因及其编码的蛋白质的研究，对于探索新的抗菌药物和开发更有效的治疗方法具有重要意义。

acrA and acrB are two commonly found bacterial genes that encode proteins critical to many Gram-negative bacteria. The proteins produced by these genes, AcrA and AcrB, along with the protein TolC, work together to form the AcrAB-TolC pump.

The AcrAB-TolC pump is a three-component complex that belongs to the resistance-nodulation-division (RND) family of antibiotic efflux pumps. This pump uses energy to expel a wide range of toxic compounds from within bacterial cells, including antibiotics, dyes, and organic solvents.

acrA and acrB play a crucial role in the antibiotic resistance of bacteria. Studies have shown that mutations or deletions in these genes can cause bacteria to become more or less susceptible to antibiotics. In addition to their role in antibiotic resistance, acrA and acrB are also involved in other biological processes such as bacterial growth and metabolism.

In clinical practice, antibiotic treatment of bacterial infections is becoming increasingly challenging due to the development of multidrug-resistant bacteria. The importance of acrA and acrB in bacterial resistance mechanisms makes them important targets for the development of new antibiotics and more effective treatments for antibiotic-resistant infections.

tetR基因是一种细菌基因，编码TetR蛋白，它是一种转录抑制因子。TetR蛋白能够结合到特定的DNA序列，称为Tet运算子，来控制其他基因的表达，包括与抗生素抗性相关的基因。

tetR基因通常存在于质粒中，这是一种与细菌染色体分离的小型环状DNA片段。质粒可以在细菌之间转移，而tetR基因在质粒中的存在可以赋予接收菌株抗生素抗性。这是因为TetR蛋白可以抑制编码抗生素降解酶或转运蛋白的基因表达，从而防止抗生素被降解或运输到细胞外。

TetR是TetR转录因子家族的一员，该家族包括其他与抗生素抗性相关的蛋白，例如MarR和QacR。这些蛋白在不同的细菌物种中高度保守，并且能够识别各种结构多样的抗生素。

除了其在抗生素抗性中的作用外，tetR基因在细菌生理中也发挥着一定的作用，例如调控生物膜形成、细胞分裂和代谢等。这表明TetR及其同源物可能具有除抗生素抗性外的其他功能。

研究tetR基因及其在细菌抗生素抗性中的作用对于开发新型抗生素和对抗抗生素抗性具有重要意义。通过了解TetR和其他转录调节因子如何控制抗生素抗性基因，研究人员可以确定新的药物开发目标，并设计新的治疗方案来克服抗生素抗性。

The tetR gene is a bacterial gene that encodes the TetR protein, a transcriptional repressor. The TetR protein binds to specific DNA sequences, known as Tet operators, to control the expression of other genes, including those involved in antibiotic resistance.

The tetR gene is commonly found in plasmids, which are small, circular pieces of DNA that are separate from the bacterial chromosome. Plasmids can be transferred between bacteria, and the presence of the tetR gene in a plasmid can confer antibiotic resistance to the recipient bacterium. This is because the TetR protein can repress the expression of genes that encode antibiotic-degrading enzymes or transporters, preventing the antibiotic from being degraded or transported out of the cell.

TetR is a member of the TetR family of transcriptional regulators, which includes other proteins involved in antibiotic resistance, such as MarR and QacR. These proteins are highly conserved across different bacterial species and can recognize a wide range of structurally diverse antibiotics.

In addition to its role in antibiotic resistance, the tetR gene has been found to play a role in bacterial physiology, such as the regulation of biofilm formation, cell division, and metabolism. This suggests that TetR and its homologues may have additional functions beyond antibiotic resistance.

The study of the tetR gene and its role in bacterial antibiotic resistance has important implications for the development of new antibiotics and strategies to combat antibiotic resistance. By understanding how TetR and other transcriptional regulators control antibiotic resistance genes, researchers can identify new targets for drug development and design new therapies that can overcome antibiotic resistance.

以下是一些在细菌中被广泛研究的基因：

• lacZ基因：lacZ基因编码β-半乳糖苷酶，参与乳糖代谢。lacZ基因的研究在细菌基因调控的研究中做出了重要贡献。

• rpoB基因：rpoB基因编码RNA聚合酶的β亚基，是基因表达所必需的。在细菌中，rpoB基因突变与抗生素耐药性有关。

• gyrA基因：gyrA基因编码DNA旋转酶的A亚基，参与DNA复制和修复。在细菌中，gyrA基因突变与抗生素耐药性有关。

• recA基因：recA基因编码参与DNA修复和重组的蛋白质。recA基因的研究对我们理解细菌中的DNA修复机制做出了重要贡献。

• ompF基因：ompF基因编码外膜蛋白质Porin，形成了革兰氏阴性菌的细胞壁通道。ompF基因的研究对我们理解细菌细胞壁的结构和功能做出了重要贡献。

• katG基因：katG基因编码过氧化物酶-催化酶，参与细菌内活性氧化物的解毒。在结核分枝杆菌中，katG基因突变与抗药性有关。

• pncA基因：pncA基因编码吡嗪酰胺酶，参与抗生素吡嗪酰胺的激活。在结核分枝杆菌中，pncA基因突变与吡嗪酰胺抗性有关。

• mtrR基因：mtrR基因编码一个转录调节因子，控制淋病奈瑟氏菌中与抗生素抗性和毒力有关的基因的表达。

• fabI基因：fabI基因编码烯酰基载体蛋白还原酶，参与细菌中的脂肪酸生物合成。FabI酶的抑制剂已经开发为一类新型抗生素。

• merA基因：merA基因编码汞还原酶，参与细菌中的汞解毒。merA基因的研究对我们理解细菌中的金属解毒机制做出了重要贡献。

Some of the well-studied genes in bacteria include:

• lacZ gene: The lacZ gene encodes the enzyme β-galactosidase, which is involved in lactose metabolism. The study of the lacZ gene has contributed significantly to our understanding of gene regulation in bacteria.

• rpoB gene: The rpoB gene encodes the β subunit of RNA polymerase, which is essential for gene expression. Mutations in the rpoB gene have been found to be associated with antibiotic resistance in bacteria.

• gyrA gene: The gyrA gene encodes the A subunit of DNA gyrase, which is involved in DNA replication and repair. Mutations in the gyrA gene have been found to be associated with antibiotic resistance in bacteria.

• recA gene: The recA gene encodes a protein involved in DNA repair and recombination. The study of the recA gene has contributed significantly to our understanding of DNA repair mechanisms in bacteria.

• ompF gene: The ompF gene encodes a porin protein that forms a channel through the outer membrane of Gram-negative bacteria. The study of the ompF gene has contributed significantly to our understanding of bacterial cell envelope structure and function.

• katG gene: The katG gene encodes the catalase-peroxidase enzyme, which is involved in the detoxification of reactive oxygen species in bacteria. Mutations in the katG gene have been found to be associated with antibiotic resistance in Mycobacterium tuberculosis, the causative agent of tuberculosis.

• pncA gene: The pncA gene encodes the pyrazinamidase enzyme, which is involved in the activation of the antibiotic pyrazinamide. Mutations in the pncA gene have been found to be associated with pyrazinamide resistance in Mycobacterium tuberculosis.

• mtrR gene: The mtrR gene encodes a transcriptional regulator that controls the expression of genes involved in antibiotic resistance and virulence in Neisseria gonorrhoeae, the causative agent of gonorrhea.

• fabI gene: The fabI gene encodes the enzyme enoyl-acyl carrier protein reductase, which is involved in fatty acid biosynthesis in bacteria. Inhibitors of the FabI enzyme have been developed as a novel class of antibiotics.

• merA gene: The merA gene encodes the mercuric reductase enzyme, which is involved in the detoxification of mercury in bacteria. The study of the merA gene has contributed significantly to our understanding of metal detoxification mechanisms in bacteria.

The study of these well-studied bacterial genes has provided valuable insights into the basic biology of bacteria, as well as the mechanisms of antibiotic resistance and the development of new antibiotics.

Here are some general statistics about the number of genes in humans, bacteria, and viruses:

• Human genes:

Humans are estimated to have between 20,000 and 25,000 protein-coding genes. However, the number of functional genes may be even higher due to alternative splicing, where a single gene can produce multiple protein variants.

• Bacterial genes:

Bacteria are unicellular organisms that have much smaller genomes than humans. The number of genes in bacteria varies depending on the species, but the average bacterial genome contains around 4,000 genes.

• Virus genes:

Viruses are much simpler organisms than bacteria or humans, and they typically have much smaller genomes. The number of genes in viruses varies widely depending on the type of virus. Some viruses have only a few genes, while others have hundreds or even thousands of genes.

It’s important to note that these numbers are approximate and can vary depending on the specific organism or virus being studied. Additionally, the number of genes does not necessarily reflect the complexity or importance of an organism or virus.

There are an estimated 10 million species of bacteria, and each species has a unique genome with a varying number of genes. However, we can still provide some general statistics about the number of genes in bacteria based on available data:

• The average number of genes in bacterial genomes is around 4,000, but this can range from a few hundred to over 15,000 depending on the species.

• The bacterium with the largest number of genes currently known is Sorangium cellulosum, with approximately 15,000 genes.

• Some bacteria have much smaller genomes than the average, such as the bacterium Carsonella ruddii, which has only 182 genes.

• Bacterial genes can be classified into core genes, which are shared by all members of a species, and accessory genes, which are unique to certain strains or species. The number of core genes in bacterial genomes is typically a few thousand, while the number of accessory genes can range from a few dozen to several thousand.

It’s worth noting that the field of microbiology is constantly evolving, and new bacteria and their genomes are being discovered all the time. As a result, these statistics are subject to change as more data becomes available.

It’s difficult to provide a comprehensive list of all core genes in bacteria, as the specific genes that are considered “core” can vary depending on the species and the methods used to identify them. However, there are some general categories of genes that are considered to be part of the bacterial core genome:

• Housekeeping genes: These are genes that are involved in basic cellular processes that are required for all cells to function, such as DNA replication, transcription, translation, and metabolism. Examples of housekeeping genes include the genes that encode ribosomal RNA (rRNA), ATP synthase, and DNA polymerase.

• Information processing genes: These are genes that are involved in the processing and transmission of genetic information, such as DNA repair genes, DNA topoisomerases, and RNA polymerase.

• Structural genes: These are genes that are involved in the formation and maintenance of cell structure, such as genes that encode cell wall components or flagella.

• Transport genes: These are genes that are involved in the transport of molecules across the cell membrane, such as ABC transporters and permeases.

• Regulatory genes: These are genes that are involved in the regulation of gene expression, such as transcription factors and sigma factors.

While these categories are a good starting point for identifying core genes in bacteria, the specific genes that are considered to be part of the core genome can vary depending on the species and the criteria used to define them. Additionally, some researchers may define “core genes” more narrowly or broadly than others, further complicating efforts to create a comprehensive list.

Housekeeping genes are essential genes that are required for basic cellular functions in all bacteria. They are involved in key processes such as DNA replication, transcription, translation, and metabolism. Here is a list of some important housekeeping genes in bacteria:

• dnaA: encodes the protein responsible for initiating DNA replication.

• gyrA: encodes DNA gyrase, an essential enzyme involved in DNA replication and repair.

• rpoB: encodes the beta subunit of RNA polymerase, which is responsible for catalyzing transcription.

• infB: encodes initiation factor 2, which is involved in translation initiation.

• recA: encodes a protein involved in DNA repair and recombination.

• groEL: encodes a chaperonin protein that assists in the folding of other proteins.

• ftsZ: encodes a protein involved in cell division.

• nrdA and nrdB: encode the subunits of ribonucleotide reductase, which is involved in nucleotide metabolism.

• atpA, atpB, atpE, and atpF: encode subunits of ATP synthase, which generates ATP during cellular respiration.

• fabF: encodes a fatty acid biosynthesis enzyme that is essential for cell membrane synthesis.

Transport genes are responsible for the movement of various molecules across the cell membrane of bacteria. These molecules can include nutrients, ions, and waste products. Here is a list of some important transport genes in bacteria:

• ABC transporters: These are a class of transporters that use ATP to move a wide range of molecules across the cell membrane, including sugars, amino acids, and vitamins. Examples of ABC transporters in bacteria include the maltose transporter (malEFG) and the histidine transporter (hisJQMP).

• PTS transporters: These transporters use a phosphate group from phosphoenolpyruvate to move sugars across the cell membrane. Examples of PTS transporters in bacteria include the glucose transporter (ptsG) and the lactose transporter (lacY).

• TonB-dependent transporters: These transporters use the energy from the proton motive force to move molecules across the outer membrane of Gram-negative bacteria. Examples of TonB-dependent transporters in bacteria include the iron transporter (fhuA) and the vitamin B12 transporter (btuB).

• Permeases: These are a class of transporters that move small molecules such as sugars, amino acids, and ions across the cell membrane. Examples of permeases in bacteria include the lactose permease (lacY) and the phosphate permease (pstS).

• MFS transporters: These transporters belong to the major facilitator superfamily and move a wide range of molecules across the cell membrane, including sugars, drugs, and organic acids. Examples of MFS transporters in bacteria include the glucose transporter (gluP) and the tetracycline transporter (tetA).

• Outer membrane porins: These are proteins that form channels in the outer membrane of Gram-negative bacteria, allowing small molecules such as nutrients and waste products to move across the membrane. Examples of outer membrane porins in bacteria include OmpF and OmpC.

These are just a few examples of important transport genes in bacteria. It’s worth noting that the specific transport genes required for cellular function can vary between different bacterial species, and some bacteria may have additional transport systems beyond those listed here.

在细菌中，有许多令人神奇的基因，但以下是其中一些最为令人惊叹的基因：

1. CRISPR-Cas9基因：CRISPR-Cas9是一种具有基因编辑能力的DNA序列，这种基因编辑技术可以用于修改细菌、植物和动物的基因，对生物医学和生物工程领域具有重大意义。

2. Green Fluorescent Protein基因：该基因来自于海葵，它的基因产物是一种能够发出绿色荧光的蛋白质，已被广泛用于生物学研究中，尤其是用于标记细胞、病原体和其他生物分子。

3. 荧光素酶基因：该基因来自于发光菌，产生一种能够发出强烈荧光的酶，已被广泛应用于生物学、生物医学和生物技术领域，例如生物传感器、荧光显微镜等。

4. Nitrogen fixation genes：固氮基因来自于一些细菌，它们能够将空气中的氮气转化为植物所需的氨基酸，对植物生长和生态系统的平衡具有重要作用。

5. Resistance genes：耐药基因是一些细菌中的基因，它们使细菌能够抵抗抗生素的杀菌作用，这些基因的存在导致了严重的公共卫生问题，需要开发新的抗生素来对抗它们。

6. Bioluminescence genes：发光基因来自于一些生物，例如发光细菌、蛤蜊和火虫等。这些基因可以使细菌产生荧光蛋白质，发出绿色、黄色、蓝色等颜色的荧光。这些细菌常常生存在深海或地下洞穴中，发光有助于它们在黑暗中进行交流或引诱猎物。

7. Denitrification genes：反硝化基因使细菌能够从硝酸盐和亚硝酸盐中释放出氮气，这些基因在土壤中具有重要作用，可帮助减少土壤中的氮含量。

8. Pili genes：纤毛基因编码一种可以使细菌产生纤毛的蛋白质，这些纤毛可以用来连接不同的细胞或附着到表面上。这些纤毛在感染性细菌中非常重要，它们帮助细菌黏附在宿主细胞上，使它们更容易入侵宿主。

9. Virulence genes：毒力基因使一些细菌具有攻击宿主细胞的能力，从而导致疾病发生。这些基因可以编码产生毒素的蛋白质，也可以编码使细菌能够避免宿主免疫系统的攻击的蛋白质。

10. Metabolism genes：代谢基因编码细菌用于生存的关键代谢途径，例如分解食物、合成细胞壁、生成能量等。这些基因在不同的细菌中有很大的差异，因此可以用于区分不同种类的细菌。

Merkel cell polyomavirus (MCPyV) is a virus that has been associated with Merkel cell carcinoma, an aggressive form of skin cancer. The MCPyV genome is small, circular, and double-stranded DNA with a length of approximately 5.4 kilobases. Here, we will provide a brief summary of the reference sequences of MCPyV isolates and the microRNA (miRNA) found in the virus.

• Reference sequence of MCPyV isolates: The reference sequence of MCPyV isolates can be found in the National Center for Biotechnology Information (NCBI) database. The NCBI’s Genome database contains information on the complete MCPyV genome, which can be accessed using the following link: https://www.ncbi.nlm.nih.gov/datasets/genomes/?taxon=493803&utm_source=nuccore&utm_medium=referral

• MCPyV isolate WaGa: The MCPyV isolate WaGa (accession number: KJ128379.1) is a strain of the virus discovered in 2014. The complete genome of this isolate can be found in the NCBI’s Nucleotide database at the following link: https://www.ncbi.nlm.nih.gov/nuccore/KJ128379.1

• MCPyV isolate MKL-1: The MCPyV isolate MKL-1 (accession number: FJ173815.1) is another strain of the virus, which was identified in 2008. The complete genome of this isolate is also available in the NCBI’s Nucleotide database and can be accessed at the following link: https://www.ncbi.nlm.nih.gov/nuccore/FJ173815.1

• miRNA: MCPyV encodes a microRNA (miRNA) known as miR-M1 (accession number: JN707599.1). miRNAs are small, non-coding RNA molecules that play important roles in regulating gene expression. The sequence of miR-M1 can be found in the NCBI’s Nucleotide database using the following link: https://www.ncbi.nlm.nih.gov/nuccore/JN707599.1

LT, LTtr, and sT are viral proteins that play critical roles in MCPyV-associated oncogenesis, specifically in the development of Merkel cell carcinoma, an aggressive form of skin cancer.

• LT (Large Tumor antigen): The Large Tumor antigen is a multifunctional protein encoded by MCPyV. It is involved in various cellular processes, including cell cycle regulation, DNA replication, and cell transformation. LT binds to the tumor suppressor protein retinoblastoma (Rb) and disrupts its function, leading to uncontrolled cell proliferation. In the context of MCPyV-associated Merkel cell carcinoma, LT expression is often observed in tumor cells, suggesting its importance in the development of this aggressive skin cancer.

• LTtr (Large Tumor antigen truncated): LTtr is a truncated version of the Large Tumor antigen, which is shorter than the full-length LT protein. This truncation results from a mutation or deletion in the viral genome, leading to a premature stop codon and an incomplete protein product. While LTtr retains some of the functions of the full-length LT, it may have altered activity or reduced functionality. The exact role of LTtr in MCPyV-associated Merkel cell carcinoma is still being investigated.

• sT, or Small Tumor antigen, is another protein encoded by Merkel Cell Polyomavirus (MCPyV) and is involved in MCPyV-related oncogenesis. sT is a multifunctional protein that plays various roles in cellular processes, including the activation of signaling pathways, modulation of protein stability, and the disruption of cellular functions that can contribute to cancer development.

  • One of the key roles of sT is its ability to interact with and inhibit protein phosphatase 2A (PP2A), a cellular tumor suppressor that negatively regulates cell growth and division. By inhibiting PP2A, sT promotes cell proliferation and survival, contributing to oncogenesis.

  • In addition to its interaction with PP2A, sT can also activate the phosphatidylinositol 3-kinase (PI3K)/Akt/mTOR signaling pathway, which further supports cell survival and growth. Furthermore, sT has been found to induce the expression of heat shock proteins, which are associated with cellular stress responses and contribute to the stabilization of oncogenic proteins.

In MCPyV-associated Merkel cell carcinoma, both Large Tumor antigen (LT) and Small Tumor antigen (sT) are expressed in tumor cells, suggesting that they cooperatively contribute to the development of this aggressive skin cancer. While LT primarily targets the retinoblastoma (Rb) tumor suppressor protein, sT interacts with multiple cellular targets to promote cell growth and survival, ultimately leading to oncogenesis.

Download the file typing_189.csv

Download the file 471.tree

library(ggtree)
library(ggplot2)

setwd("/media/jhuang/Elements2/Data_Anna_C.acnes/plotTreeHeatmap/")

# -- edit tree --
#https://icytree.org/
#0.000780
info <- read.csv("typing_189.csv")
info$name <- info$Isolate
#tree <- read.tree("core_gene_alignment_fasttree_directly_from_186isoaltes.tree")  --> NOT GOOD!
tree <- read.tree("471.tree")
cols <- c(infection='purple2', commensalism='skyblue2')     

library(dplyr)
heatmapData2 <- info %>% select(Isolate, ST, Clonal.Complex, Phylotype)
rn <- heatmapData2$Isolate
heatmapData2$Isolate <- NULL
heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
rownames(heatmapData2) <- rn

#https://bookdown.org/hneth/ds4psy/D-3-apx-colors-basics.html
heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red",  "navyblue", "gold",     "green","orange","pink","purple","magenta","brown", "darksalmon","chocolate4","darkkhaki", "lightcyan3", "maroon","lightgreen",     "blue","cyan", "skyblue2", "azure3","blueviolet","darkgoldenrod",  "tomato","mediumpurple4","indianred", 
                      "cornflowerblue","darkgreen","seagreen3","tan","red","green","orange","pink","brown","magenta",     "cornflowerblue","darkgreen","red","tan","brown",      "darkgrey")
names(heatmap.colours) <- c("1","2","3","4","5", "6","7",   "20","21","22", "28","30","33","42","43","52","53", "66","68",    "100","105","124","133","134","135","137",     "159","161",    "CC1","CC2","CC3","CC4","CC5","CC6","CC30","CC72","CC77","Singleton",    "IA1","IA2","IB","II","III",    "NA")
#mydat$Regulation <- factor(mydat$Regulation, levels=c("up","down"))

#circular
p <- ggtree(tree, layout='circular', branch.length='none') %<+% info + 
  geom_tippoint(aes(color=Type)) + 
  scale_color_manual(values=cols) + geom_tiplab2(aes(label=name), offset=1)
#, geom='text', align=TRUE,  linetype=NA, hjust=1.8,check.overlap=TRUE, size=3.3
#difference between geom_tiplab and geom_tiplab2?
#+ theme(axis.text.x = element_text(angle = 30, vjust = 0.5)) + theme(axis.text = element_text(size = 20))  + scale_size(range = c(1, 20))
#font.size=10, 
png("ggtree.png", width=1260, height=1260)
svg("ggtree.svg", width=1260, height=1260)
p
dev.off()

#png("ggtree_and_gheatmap.png", width=1290, height=1000)
#svg("ggtree_and_gheatmap.svg", width=1290, height=1000)
svg("ggtree_and_gheatmap.svg", width=17, height=15)
gheatmap(p, heatmapData2, width=0.1,colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=4, offset = 8) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 14)) + theme(legend.title = element_text(size = 14)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))  
dev.off()

Download the file Bubble_R_allTantigens.csv

library(ggplot2)
library(dplyr)
library(magrittr)
library(tidyr)
library(forcats)

mydat <- read.csv("Bubble_R_allTantigens.csv", sep=";", header=TRUE)
mydat$GeneRatio <- sapply(mydat$GeneRatio_frac, function(x) eval(parse(text=x)))
#mydat$FoldEnrichment <- as.numeric(mydat$FoldEnrichment)
mydat$Regulation <- factor(mydat$Regulation, levels=c("up","down"))
mydat$Comparison <- factor(mydat$Comparison, levels=c("sT vs ctrl d3","sT vs ctrl d8","LT vs ctrl d3","LT vs ctrl d8","LTtr vs ctrl d3","LTtr vs ctrl d8","sT+LT vs ctrl d3","sT+LTtr vs ctrl d912")) 
mydat$Term <- factor(mydat$Term, levels=rev(c("Cell division", "Cell cycle", "Negative regulation of cell proliferation", "Mitotic cell cycle", "Mitotic sister chromatid segregation", "Mitotic spindle organization", "Chromosome segregation", "DNA replication", "DNA repair", "Cellular response to DNA damage stimulus", "Regulation of transcription, DNA-templated", "Positive regulation of transcription, DNA-templated", "Regulation of transcription from RNA polymerase II promoter", "Negative regulation of transcription from RNA polymerase II promoter", "rRNA processing", "Protein folding", "Immune response", "Inflammatory response", "Positive regulation of I-kappaB kinase/NF-kappaB signaling", "Cellular response to tumor necrosis factor", "Chemotaxis", "Neutrophil chemotaxis", "Innate immune response", "Response to virus", "Defense response to virus", "Cellular response to lipopolysaccharide", "Signal transduction", "Response to drug", "Apoptotic process", "Cell adhesion", "Collagen fibril organization", "Nervous system development", "Axon guidance", "Extracellular matrix organization", "Angiogenesis"))) 
tiff("Bubble_all-Tantigens_big.tiff", units = "in", width = 35, height = 50, res=500) 
#png("bubble.png", width=1400, height=600)

xl <- factor(rev(c("Cell division", "Cell cycle", "Negative regulation of cell proliferation", "Mitotic cell cycle", "Mitotic sister chromatid segregation", "Mitotic spindle organization", "Chromosome segregation", "DNA replication", "DNA repair", "Cellular response to DNA damage stimulus", "Regulation of transcription, DNA-templated", "Positive regulation of transcription, DNA-templated", "Regulation of transcription from RNA polymerase II promoter", "Negative regulation of transcription from RNA polymerase II promoter", "rRNA processing", "Protein folding", "Immune response", "Inflammatory response", "Positive regulation of I-kappaB kinase/NF-kappaB signaling", "Cellular response to tumor necrosis factor", "Chemotaxis", "Neutrophil chemotaxis", "Innate immune response", "Response to virus", "Defense response to virus", "Cellular response to lipopolysaccharide", "Signal transduction", "Response to drug", "Apoptotic process", "Cell adhesion", "Collagen fibril organization", "Nervous system development", "Axon guidance", "Extracellular matrix organization", "Angiogenesis")))
bold.terms <- c("Innate immune response", "Response to virus", "Defense response to virus")
bold.labels <- ifelse((xl) %in% bold.terms, yes = "bold", no = "plain")

#-log10(FDR) can be renamed as 'Significance'   
png("bubble_plot.png", 3000, 2000)
ggplot(mydat, aes(y = Term, x = Comparison)) + geom_point(aes(color = Regulation, size = Count, alpha = abs(log10(FDR)))) + scale_color_manual(values = c("up" = "red", "down" = "blue")) + scale_size_continuous(range = c(1, 34)) + labs(x = "", y = "", color="Regulation", size="Count", alpha="-log10(FDR)") + theme(axis.text.y = element_text(face = bold.labels))+ theme(axis.text.x = element_text(angle = 30, vjust = 0.5)) + theme(axis.text = element_text(size = 40)) + theme(legend.text = element_text(size = 40)) + theme(legend.title = element_text(size = 40))+
  guides(color = guide_legend(override.aes = list(size = 20)), alpha = guide_legend(override.aes = list(size = 20)))
dev.off()

智力是由多个基因、环境因素及其相互作用共同影响的复杂性状。尽管没有单一的“智力基因”，但研究人员已经发现了一些与认知能力相关的基因。这些基因包括：

• CHRM2：这个基因编码乙酰胆碱受体 2（cholinergic receptor, muscarinic 2），与认知能力（包括智力和记忆力）相关。

• BDNF：脑源性神经营养因子（Brain-derived neurotrophic factor，BDNF）是一种与神经元生长和维持有关的蛋白质。BDNF 基因的变异与智力、记忆和学习差异有关。

• COMT：儿茶酚氧位甲基转移酶（catechol-O-methyltransferase，COMT）基因参与多巴胺和去甲肾上腺素等神经递质的分解。COMT 基因的某些变异与认知能力和工作记忆差异有关。

• SNAP25：突触小泡相关蛋白 25（Synaptosomal-associated protein 25，SNAP25）参与突触处神经递质的释放。SNAP25 基因的变异与智力和认知能力相关。

• ASPM：异常纺锤体样小头畸形相关（abnormal spindle-like microcephaly-associated，ASPM）基因与大脑大小有关，并与智力相关。该基因的变种与认知能力差异有关。

• NRG1：神经胶质瘤 1（Neuregulin 1，NRG1）参与神经元发育，其基因变异与认知功能和智力有关。

需要注意的是，智力是一个多面的特质，许多基因以复杂的方式共同影响它。此外，环境因素和基因-环境相互作用在决定个体智力方面也起着重要作用。随着我们对智力基因基础的理解不断深入，可能会发现更多基因及其在认知功能中的作用。

Intelligence is a complex trait influenced by multiple genes, environmental factors, and their interactions. Although there is no single “intelligence gene,” researchers have identified several genes that appear to be associated with cognitive abilities. Some of these genes include:

• CHRM2: This gene encodes the cholinergic receptor, muscarinic 2, and has been associated with cognitive abilities, including general intelligence and memory.

• BDNF: Brain-derived neurotrophic factor (BDNF) is a protein involved in the growth and maintenance of neurons. Variations in the BDNF gene have been linked to differences in intelligence, memory, and learning.

• COMT: The catechol-O-methyltransferase (COMT) gene is involved in the breakdown of neurotransmitters such as dopamine and norepinephrine. Certain variations in the COMT gene have been associated with differences in cognitive performance and working memory.

• SNAP25: Synaptosomal-associated protein 25 (SNAP25) is involved in the release of neurotransmitters at synapses. Genetic variations in SNAP25 have been linked to intelligence and cognitive performance.

• ASPM: The abnormal spindle-like microcephaly-associated (ASPM) gene plays a role in brain size and has been associated with intelligence. Variants of this gene have been linked to differences in cognitive abilities.

• NRG1: Neuregulin 1 (NRG1) is involved in neuron development, and genetic variations in this gene have been associated with cognitive function and intelligence.

It is essential to note that intelligence is a multifaceted trait, and many genes contribute to it in complex ways. Additionally, environmental factors and gene-environment interactions also play a significant role in determining an individual’s intelligence. As our understanding of the genetic basis of intelligence continues to grow, more genes and their roles in cognitive function will likely be identified.