20210201

Contents
  1. 1. Working directories
  2. 2. Downloading
  3. 3. p62 Draft
    1. 3.1. Additional references
    2. 3.2. Chemicals, activators of Nrf2
  4. 4. Ensembl-Ids vs Entrez-Ids
  5. 5. Human Protein Atlas
  6. 6. Gene ID
  7. 7. Database download
  8. 8. FASTQ Analysis
  9. 9. App recommended to GYF
  10. 10. Gender determination from RAN-Seq

Working directories

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i=/media/ht/ht_5T_5/HLA-G/SRA/Summary/Genetic_Mechanisms_of_Sex_Determination.docx
setsid wps ${i}
#
i=/media/ht/ht_5T/Database/Ensembl
pcmanfm -n ${i}; cd ${i} # Human from Ensembl, downloading
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/Summary/E-MTAB-1733.xlsx
setsid wps ${i} # Summary of E-MTAB-1733
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/GZ
pcmanfm -n ${i}; cd ${i} # FASTQ Magicblast

Downloading

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wget -rnp ftp://ftp.ensembl.org/pub/release-102/mysql/homo_sapiens_variation_102_38/
#
i=wget -rnp ftp://ftp.ensembl.org/pub/release-102/mysql/homo_sapiens_variation_102_38/
wget -rnp ${i}

p62 Draft

Additional references

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i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_2/Ref2
pcmanfm -n ${i}; cd ${i} # Additional references
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Ref_201_Molecular_mechanisms_of_HPV_mediated_neoplastic_progression.pdf
Ref_203_New_Insights_in_the_Pathogenesis_of_HPV_Infection_and_the_Associated_Carcinogenic_Processes_The_Role_of_Chronic_Inflammation_and_Oxidative_Stress.pdf
Ref_208_Cancer__Oxidative_Stress_and_Metastasis.pdf
Ref_209_Stress-sensing_mechanisms_and_the_physiological_roles_of_the_Keap1–Nrf2_system_during_cellular_stress.pdf
Ref_210_Anti-Viral_Potential_and_Modulation_of_Nrf2_by_Curcumin-_Pharmacological_Implications.pdf
Ref_211_CDDO-Me_Sulforaphane_and_tBHQ_attenuate_the_RANKLinduced_osteoclast_differentiation_via_activating_the_NRF2-_mediated_antioxidant_response.pdf
Ref_213_Human_papillomavirus_type_18_E5_oncoprotein_cooperates_with_E6_and_E7_in_promoting_cell_viability_and_invasion_and_in_modulating_the_cellular_redox_state.pdf
Ref_214_NRF2_promotes_tumor_maintenance_by_modulating_mRNA_translation_in_pancreatic_cancer.pdf
Ref_215_Nrf2_in_cancers-_A_double‐edged_sword.pdf
Ref_216_Nuclear_lactate_dehydrogenase_A_senses_ROS_to_produce_α-hydroxybutyrate_for_HPV-induced_cervical_tumor_growth.pdf
Ref_217_Regulation_of_Nrf2_–_An_update.pdf

Chemicals, activators of Nrf2

  • N,N‐dimethylformamide/Dimethylformamide (DMF)
  • sulforaphane (SFN)
  • Tert-butylhydroquinone (tBHQ)
  • CDDO-Im/CDDO-imidazolide

Ensembl-Ids vs Entrez-Ids

Human Protein Atlas

Gene ID

How to get Gene ID from Ensembl?
3. You can download gene ID data from BioMart. Select Ensembl Genes 99 –> Human genes –> Attributes –> GENE –> External References –> select HGNC symbol and NCBI gene ID –> Results.

  • Help - Homo_sapiens - Ensembl genome browser 102
    • Name - from official gene nomenclature commitees such as HGNC (for human) and MGI (for mouse)
    • CCDS - coding sequence IDs from the Consensus Coding Sequence Set
    • UniProtKB - protein IDs from UniProtKB that match one of the translations of this gene
    • RefSeq - Indicates if the gene has transcript(s) identified as MANE.
    • LRG - IDs from the Locus Reference Genomic (LRG) project matching the Ensembl gene
    • Ensembl version - versioning of the Ensembl gene ID
    • GRCh37 assembly - (for human only) with genomic coordinates and links to the Location and Gene views of the gene on the previous human assembly
    • Gene type - The gene type includes both status (e.g. known) and biotype (e.g. protein coding)
    • Annotation method - It can be the Ensembl automatic, Havana manual or a merge between automatic and manual (for human, mouse, zebrafish, pig, and rat)
    • Alternative genes - IDs from the HAVANA project that match the Ensembl gene

FASTQ Analysis

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i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/GZ/1
pcmanfm -n ${i}; cd ${i} # 
#
function MG { # FASTQ.GZ
	for FQ in ../*_1.fastq.gz; do Read1="${FQ}"; Read2="${FQ%_*}_2.fastq.gz"; Filename=`basename ${FQ}`; BAM="${Filename%_*}_vs_`basename ${DB}`.bam"; magicblast -num_threads 2 -db ${DB} -infmt fastq -query ${Read1} -query_mate ${Read2} | samtools view -bS -> "${BAM}"; samtools sort ${BAM} > "${BAM%.bam}.sort.bam"; samtools index "${BAM%.bam}.sort.bam"; bedtools bamtofastq -i ${BAM} -fq "${Read1%.fastq.gz}.fq" -fq2 "${Read2%.fastq.gz}.fq"; pigz "${Read1%.fastq.gz}.fq" "${Read2%.fastq.gz}.fq"; done
}
#############################################
SRA_Path=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/GZ/1
i=Essential
mkdir ${i}; cd ${i}
#
DB="/media/ht/ht_5T_5/HLA-G/SRA/DB/Essential/Human_Essential"
MG

App recommended to GYF

Gender determination from RAN-Seq

  • XIST
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i <- "/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/Summary/E-MTAB-1733.xlsx"
x <- data.frame(read_excel(i, sheet = "FRKM_All"))
names(x)[1] <- "Ensembl.gene.ID"
#
i <- "/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/Summary/Supp_Info/FPKM_allsamples.txt"
x <- read.csv(i, sep = "\t")
i <- "/home/ht/Downloads/Gender_Gene.list"
y <-  read.csv(i, header = TRUE, sep = "\t")
Gene <- data.frame(y[, c(12,7)])
y <- merge(Gene, x, by = "Ensembl.gene.ID", all.x = TRUE)
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