Identification of key gene modules and pathways of human platelet transcriptome in acute myocardial infarction patients through co-expression network

stjosephs-hospital

Acute myocardial infarction (AMI) seriously threatens human life. In this study we aimed to systemically analyze the function of key gene modules in human platelets in AMI. We used weighted gene co-expression network analysis (WGCNA) to construct a co-expression module, and analyzed the relationship between potential modules and clinical characteristics based on platelet RNA-seq RPKM count reads of 16 ST-segment elevation myocardial infarction (STEMI) patients and 16 non-STEMI (NSTEMI) patients provided by the GEO database.

Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed with the DAVID tool. Hub genes were calculated by the Cytohubba package. A total of 3653 genes was selected to construct the co-expression modules.

A significant correlation between BMI and the module with color of sky-blue in STEMI. In NSTEMI, there was a significant correlation between the sky blue module and CAD, the Salmon module and HT, and the Cyan module and HT. In STEMI, the Hub genes were mainly enriched in functions related to cell membrane signal transduction including Aqp1, Armcx1, Gsta4, Hist3h2a and Il17re.

In NSTEMI, the Hub genes are related mainly to energy metabolism in the sky-blue module including Olr1, Nap1l3, Gfer, Dohh, Crispld1 and Ccdc8b; they are mainly related to extracellular space and calcium binding in the Cyan module, including Clec12b, Chd4, Asgr1, Armcx4, Chid1 and Alkbh7.

The hub genes in the Salmon module include Ell3, Aldh1b1, Cavin4, Cabp4, Eif1ay and Dus3l. Our results provide a framework for co-expression gene modules in STEMI and NSTEMI patients, and identify key targets as biomarkers for patients with different subtypes of AMI.

Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S

In response to COVID-19, the international water community rapidly developed methods to quantify the SARS-CoV-2 genetic signal in untreated wastewater. Wastewater surveillance using such methods has the potential to complement clinical testing in assessing community health. This interlaboratory assessment evaluated the reproducibility and sensitivity of 36 standard operating procedures (SOPs), divided into eight method groups based on sample concentration approach and whether solids were removed.

Two raw wastewater samples were collected in August 2020, amended with a matrix spike (betacoronavirus OC43), and distributed to 32 laboratories across the U.S. Replicate samples analyzed in accordance with the project’s quality assurance plan showed high reproducibility across the 36 SOPs: 80% of the recovery-corrected results fell within a band of ±1.15 log10 genome copies per L with higher reproducibility observed within a single SOP (standard deviation of 0.13 log10).

The inclusion of a solids removal step and the selection of a concentration method did not show a clear, systematic impact on the recovery-corrected results. Other methodological variations (e.g., pasteurization, primer set selection, and use of RT-qPCR or RT-dPCR platforms) generally resulted in small differences compared to other sources of variability.

These findings suggest that a variety of methods are capable of producing reproducible results, though the same SOP or laboratory should be selected to track SARS-CoV-2 trends at a given facility. The methods showed a 7 log10 range of recovery efficiency and limit of detection highlighting the importance of recovery correction and the need to consider method sensitivity when selecting methods for wastewater surveillance.

stjosephs-hospital

stjosephs-hospital

ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs

Motivation: Access to large-scale genomics and transcriptomics data from various tissues and cell lines allowed the discovery of wide-spread alternative splicing events and alternative promoter usage in mammalians. Between human and mouse, gene-level orthology is currently present for nearly 16k protein-coding genes spanning a diverse repertoire of over 200k total transcript isoforms.

Results: Here, we describe a novel method, ExTraMapper, which leverages sequence conservation between exons of a pair of organisms and identifies a fine-scale orthology mapping at the exon and then transcript level. ExTraMapper identifies more than 350k exon mappings, as well as 30k transcript mappings between human and mouse using only sequence and gene annotation information.

We demonstrate that ExTraMapper identifies a larger number of exon and transcript mappings compared to previous methods. Further, it identifies exon fusions, splits, and losses due to splice site mutations, and finds mappings between microexons that are previously missed.

By reanalysis of RNA-seq data from 13 matched human and mouse tissues, we show that ExTraMapper improves the correlation of transcript-specific expression levels suggesting a more accurate mapping of human and mouse transcripts. We also applied the method to detect conserved exon and transcript pairs between human and rhesus macaque genomes to highlight the point that ExTraMapper is applicable to any pair of organisms that have orthologous gene pairs.

Availability: The source code and the results are available

Unconventional viral gene expression mechanisms as therapeutic targets

Unlike the human genome that comprises mostly noncoding and regulatory sequences, viruses have evolved under the constraints of maintaining a small genome size while expanding the efficiency of their coding and regulatory sequences.

As a result, viruses use strategies of transcription and translation in which one or more of the steps in the conventional gene-protein production line are altered. These alternative strategies of viral gene expression (also known as gene recoding) can be uniquely brought about by dedicated viral enzymes or by co-opting host factors (known as host dependencies).

Targeting these unique enzymatic activities and host factors exposes vulnerabilities of a virus and provides a paradigm for the design of novel antiviral therapies. In this Review, we describe the types and mechanisms of unconventional gene and protein expression in viruses, and provide a perspective on how future basic mechanistic work could inform translational efforts that are aimed at viral eradication.

 

anti- GCNF antibody

FNab03390 100µg
EUR 606.3
Description: Antibody raised against GCNF

GCNF Conjugated Antibody

C48479 100ul
EUR 476.4

Germ Cell Nuclear Factor (GCNF) Antibody

20-abx131389
  • EUR 510.00
  • EUR 159.60
  • EUR 1446.00
  • EUR 693.60
  • EUR 393.60
  • 100 ug
  • 10 ug
  • 1 mg
  • 200 ug
  • 50 ug

Polyclonal NR6A1 / GCNF Antibody (Ligand-binding Domain)

AMM06820G 0.05mg
EUR 580.8
Description: A polyclonal antibody raised in Rabbit that recognizes and binds to Human NR6A1 / GCNF (Ligand-binding Domain). This antibody is tested and proven to work in the following applications:

GCNF (anti human nuclear recepter antibody, clone# H7921)

PP-H7921-00 0.1mg/100uL
EUR 747.6
Description: The GCNF (anti human nuclear recepter antibody, clone# H7921) is available in Europe and for worldwide shipping via Gentaur.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human)

4-PAC509Hu01
  • EUR 296.40
  • EUR 3012.00
  • EUR 750.00
  • EUR 372.00
  • EUR 256.80
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF)

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), PE

4-PAC509Hu01-PE
  • EUR 355.20
  • EUR 3168.00
  • EUR 900.00
  • EUR 446.40
  • EUR 234.00
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with PE.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), APC

4-PAC509Hu01-APC
  • EUR 414.00
  • EUR 3930.00
  • EUR 1094.40
  • EUR 528.00
  • EUR 262.80
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with APC.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), Cy3

4-PAC509Hu01-Cy3
  • EUR 502.80
  • EUR 5190.00
  • EUR 1410.00
  • EUR 654.00
  • EUR 301.20
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with Cy3.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), HRP

4-PAC509Hu01-HRP
  • EUR 379.20
  • EUR 3426.00
  • EUR 968.40
  • EUR 477.60
  • EUR 247.20
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with HRP.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), FITC

4-PAC509Hu01-FITC
  • EUR 355.20
  • EUR 3168.00
  • EUR 900.00
  • EUR 446.40
  • EUR 234.00
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with FITC.

GCNF ELISA KIT|Human

EF009808 96 Tests
EUR 826.8

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), Biotinylated

4-PAC509Hu01-Biotin
  • EUR 373.20
  • EUR 2952.00
  • EUR 872.40
  • EUR 457.20
  • EUR 262.80
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with Biotin.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), APC-Cy7

4-PAC509Hu01-APC-Cy7
  • EUR 685.20
  • EUR 7716.00
  • EUR 2046.00
  • EUR 912.00
  • EUR 382.80
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with APC-Cy7.

Recombinant Germ Cell Nuclear Factor (GCNF)

4-RPC509Hu01
  • EUR 560.83
  • EUR 273.60
  • EUR 1773.12
  • EUR 671.04
  • EUR 1222.08
  • EUR 451.20
  • EUR 4252.80
  • 100 ug
  • 10ug
  • 1 mg
  • 200 ug
  • 500 ug
  • 50ug
  • 5 mg
Description: Recombinant Human Germ Cell Nuclear Factor expressed in: E.coli

Anti-GCNF antibody

PAab03390 100 ug
EUR 426

Human Germ Cell Nuclear Factor (GCNF) Protein

20-abx650014
  • EUR 777.60
  • EUR 326.40
  • EUR 2397.60
  • EUR 927.60
  • EUR 560.40
  • 100 ug
  • 10 ug
  • 1 mg
  • 200 ug
  • 50 ug

anti-GCNF

YF-PA23769 50 ul
EUR 400.8
Description: Mouse polyclonal to GCNF

anti-GCNF

YF-PA11986 50 ul
EUR 435.6
Description: Mouse polyclonal to GCNF

anti-GCNF

YF-PA11987 50 ug
EUR 435.6
Description: Mouse polyclonal to GCNF

anti-GCNF

YF-PA11988 100 ul
EUR 483.6
Description: Rabbit polyclonal to GCNF

anti-GCNF

YF-PA11989 100 ug
EUR 483.6
Description: Rabbit polyclonal to GCNF

Anti-KAT2A / GCN5 (3F8)

YF-MA10372 100 ug
EUR 435.6
Description: Mouse monoclonal to KAT2A / GCN5

Anti-KAT2A / GCN5 (4F9)

YF-MA13213 100 ug
EUR 435.6
Description: Mouse monoclonal to KAT2A / GCN5

GCN5 (GCN5) Antibody

abx233389-100ug 100 ug
EUR 610.8

GCN5 (GCN5) Antibody

20-abx007509
  • EUR 360.00
  • EUR 526.80
  • EUR 226.80
  • 100 ul
  • 200 ul
  • 30 ul

GCN2 Antibody

49575-100ul 100ul
EUR 399.6

GCN2 Antibody

49575-50ul 50ul
EUR 286.8

GCN5 antibody

70R-51548 100 ul
EUR 292.8
Description: Purified Polyclonal GCN5 antibody

GCN2 Antibody

DF7801 200ul
EUR 420

GCN1 Antibody

DF15941 100ul
EUR 420

GCN5 Antibody

F40091-0.08ML 0.08 ml
EUR 140.25
Description: GCN5 functions as a histone acetyltransferase (HAT) to promote transcriptional activation. Acetylation of histones gives a specific tag for epigenetic transcription activation. This protein has significant histone acetyltransferase activity with core histones, but not with nucleosome core particles.

GCN5 Antibody

F40091-0.4ML 0.4 ml
EUR 322.15
Description: GCN5 functions as a histone acetyltransferase (HAT) to promote transcriptional activation. Acetylation of histones gives a specific tag for epigenetic transcription activation. This protein has significant histone acetyltransferase activity with core histones, but not with nucleosome core particles.

GCN5 Antibody

F41987-0.08ML 0.08 ml
EUR 140.25
Description: KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. It also functions as a repressor of NF-kappa-B by promoting ubiquitination of the NF-kappa-B subunit RELA in a HAT-independent manner.

GCN5 Antibody

F41987-0.4ML 0.4 ml
EUR 322.15
Description: KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. It also functions as a repressor of NF-kappa-B by promoting ubiquitination of the NF-kappa-B subunit RELA in a HAT-independent manner.

GCN2 Antibody

F50133-0.4ML 0.4 ml
EUR 322.15
Description: GCN2 (EIF2AK4) belongs to a family of kinases that phosphorylate the alpha subunit of eukaryotic translation initiation factor-2 to downregulate protein synthesis in response to varied cellular stresses.

GCN2 Antibody

R31137 100 ug
EUR 356.15
Description: Eukaryotic Translation Initiation Factor 2-Alpha Kinase 4, also called GCN2 (General control nonderepressible 2), is an enzyme that in humans is encoded by the EIF2AK4 gene. It belongs to a family of kinases that phosphorylate the alpha subunit of eukaryotic translation initiation factor-2 to downregulate protein synthesis in response to varied cellular stresses. Hartz(2005) mapped the gene to chromosome 15q15.1 based on an alignment of the protein sequence with the genomic sequence. Berlanga et al.(1999) demonstrated that GCN2 immunopurified from mouse liver extracts could phosphorylate rabbit Eif2 in vitro. Serum starvation increased the level of phosphorylated EIF2-alpha more than 2-fold in human embryonic kidney cells transfected with mouse Eif2ak4. Costa-Mattioli et al.(2005) reported a unique feature of hippocampal slices from GCN2-null mice: in CA1, a single 100-Hz train induced a strong and sustained long-term potentiation(late LTP or L-LTP), which was dependent on transcription and translation.

pGL4.19-TA-GCNF response element Plasmid

PVTB00989-2a 2 ug
EUR 427.2

GCN5L2 antibody

10R-1171 100 ul
EUR 379.2
Description: Mouse monoclonal GCN5L2 antibody

GCN5L2 antibody

10R-1647 100 ug
EUR 614.4
Description: Mouse monoclonal GCN5L2 antibody

GCN5L2 antibody

70R-32048 100 ug
EUR 392.4
Description: Rabbit polyclonal GCN5L2 antibody

GCN5L2 Antibody

ABD3383 100 ug
EUR 525.6

GCN5L2 Antibody

DF3383 200ul
EUR 420

anti- GCN5 antibody

FNab03389 100µg
EUR 658.5
Description: Antibody raised against GCN5

GCN2 (pT899) Antibody

abx215104-100ug 100 ug
EUR 526.8

GCN5 Antibody / KAT2A

R32295 100 ug
EUR 356.15
Description: Histone acetyltransferase KAT2A, also called GCN5 and GCN5L2, is an enzyme that in humans is encoded by the KAT2A gene. It is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. The GCN5 protein, a regulator of transcription activation in yeast, promotes maximal levels of transcription by 2 transcriptional activators, GCN4 and the HAP2-HAP3-HAP4 complex. The GCN4 protein activates transcription of a large number of amino acid biosynthetic genes under limiting amino acid conditions and the HAP2-HAP3-HAP4 complex is thought to mediate transcription of genes involved in respiratory functions. GCN5 also functions as a repressor of NF-kappa-B by promoting ubiquitination of the NF-kappa-B subunit RELA in a HAT-independent manner.

GCN2-Like Protein (GCN2) Antibody

20-abx225156
  • EUR 444.00
  • EUR 727.20
  • EUR 376.80
  • 100 ul
  • 200 ul
  • 50 ul

EIF2AK4 Antibody (GCN2)

F50133-0.08ML 0.08 ml
EUR 140.25
Description: GCN2 (EIF2AK4) belongs to a family of kinases that phosphorylate the alpha subunit of eukaryotic translation initiation factor-2 to downregulate protein synthesis in response to varied cellular stresses.

EIF2AK4 Antibody / GCN2

RQ5721 100 ug
EUR 356.15
Description: EIF2AK4 (Eukaryotic Translation Initiation Factor 2-Alpha Kinase 4), also called GCN2, is an enzyme that in humans is encoded by the EIF2AK4 gene. EIF2AK4 belongs to a family of kinases that phosphorylate the alpha subunit of eukaryotic translation initiation factor-2 to downregulate protein synthesis in response to varied cellular stresses. Hartz(2005) mapped the EIF2AK4 gene to chromosome 15q15.1 based on an alignment of the EIF2AK4 sequence with the genomic sequence. Berlanga et al.(1999) demonstrated that Gcn2 immunopurified from mouse liver extracts could phosphorylate rabbit Eif2 in vitro. Serum starvation increased the level of phosphorylated EIF2-alpha more than 2-fold in human embryonic kidney cells transfected with mouse Eif2ak4. Costa-Mattioli et al.(2005) reported a unique feature of hippocampal slices from Gcn2-null mice: in CA1, a single 100-Hz train induced a strong and sustained long-term potentiation(late LTP or L-LTP), which was dependent on transcription and translation.

Polyclonal GCN2 Antibody

APR16096G 0.05ml
EUR 580.8
Description: A polyclonal antibody raised in Rabbit that recognizes and binds to Human GCN2 . This antibody is tested and proven to work in the following applications:

GCN2 Conjugated Antibody

C49575 100ul
EUR 476.4

GCN5 Polyclonal Antibody

40956-100ul 100ul
EUR 302.4

GCN5 Polyclonal Antibody

40956-50ul 50ul
EUR 224.4

GCN5 Polyclonal Antibody

A-4013
  • EUR 740.34
  • EUR 235.40
  • EUR 383.90
  • 100 µg
  • 50 ul
  • 100 ul

GCN5 Polyclonal Antibody

ABP51410-003ml 0.03ml
EUR 189.6
Description: A polyclonal antibody for detection of GCN5 from Human, Mouse. This GCN5 antibody is for WB, IHC-P, ELISA. It is affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogenand is unconjugated. The antibody is produced in rabbit by using as an immunogen synthesized peptide derived from the C-terminal region of human GCN5 at AA range: 660-740

GCN5 Polyclonal Antibody

ABP51410-01ml 0.1ml
EUR 346.8
Description: A polyclonal antibody for detection of GCN5 from Human, Mouse. This GCN5 antibody is for WB, IHC-P, ELISA. It is affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogenand is unconjugated. The antibody is produced in rabbit by using as an immunogen synthesized peptide derived from the C-terminal region of human GCN5 at AA range: 660-740

GCN5 Polyclonal Antibody

ABP51410-02ml 0.2ml
EUR 496.8
Description: A polyclonal antibody for detection of GCN5 from Human, Mouse. This GCN5 antibody is for WB, IHC-P, ELISA. It is affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogenand is unconjugated. The antibody is produced in rabbit by using as an immunogen synthesized peptide derived from the C-terminal region of human GCN5 at AA range: 660-740

GCN2 Polyclonal Antibody

ABP55272-003ml 0.03ml
EUR 189.6
Description: A polyclonal antibody for detection of GCN2 from Human, Mouse. This GCN2 antibody is for IHC-P, ELISA. It is affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogenand is unconjugated. The antibody is produced in rabbit by using as an immunogen synthesized peptide derived from human GCN2 around the non-phosphorylation site of T899

GCN2 Polyclonal Antibody

ABP55272-01ml 0.1ml
EUR 346.8
Description: A polyclonal antibody for detection of GCN2 from Human, Mouse. This GCN2 antibody is for IHC-P, ELISA. It is affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogenand is unconjugated. The antibody is produced in rabbit by using as an immunogen synthesized peptide derived from human GCN2 around the non-phosphorylation site of T899

GCN2 Polyclonal Antibody

ABP55272-02ml 0.2ml
EUR 496.8
Description: A polyclonal antibody for detection of GCN2 from Human, Mouse. This GCN2 antibody is for IHC-P, ELISA. It is affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogenand is unconjugated. The antibody is produced in rabbit by using as an immunogen synthesized peptide derived from human GCN2 around the non-phosphorylation site of T899

GCN5 Polyclonal Antibody

ES2409-100ul 100ul
EUR 334.8
Description: A Rabbit Polyclonal antibody against GCN5 from Human/Mouse. This antibody is tested and validated for WB, ELISA, IHC, WB, ELISA

GCN5 Polyclonal Antibody

ES2409-50ul 50ul
EUR 248.4
Description: A Rabbit Polyclonal antibody against GCN5 from Human/Mouse. This antibody is tested and validated for WB, ELISA, IHC, WB, ELISA

GCN2 Polyclonal Antibody

ES6271-100ul 100ul
EUR 334.8
Description: A Rabbit Polyclonal antibody against GCN2 from Human/Mouse. This antibody is tested and validated for IHC, WB, ELISA

GCN2 Polyclonal Antibody

ES6271-50ul 50ul
EUR 248.4
Description: A Rabbit Polyclonal antibody against GCN2 from Human/Mouse. This antibody is tested and validated for IHC, WB, ELISA

Anti-KAT2A/GCN5 Antibody

PB9713 100ug/vial
EUR 352.8

GCN1L1 Polyclonal Antibody

27884-100ul 100ul
EUR 302.4

GCN1L1 Polyclonal Antibody

27884-50ul 50ul
EUR 224.4

GCN1L1 Polyclonal Antibody

A73411
  • EUR 377.30
  • EUR 577.50
  • 50 ul
  • 100 ul

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