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141
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ShareScore release 0.9.0
Dataset results
141 results for “MHC class I”
Type I interferon activates MHC class I-dressed CD11b+ conventional dendritic cells to promote protective anti-tumor CD8+ T cell immunity
GEO Series GSE181939. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
GEO Series GSE205588. Homo sapiens. 8 samples. Type: Other.
Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Spatial
GEO Series GSE289170. Mus musculus. 6 samples. Type: Other.
Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses
GEO Series GSE189773. Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance
GEO Series GSE114484. Homo sapiens. 14 samples. Type: Expression profiling by array.
Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses [RNA-Seq]
GEO Series GSE189772. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Type I interferon activates MHC class I-dressed CD11b+ conventional dendritic cells to promote protective anti-tumor CD8+ T cell immunity
GEO Series GSE151990. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
ZBTB32 Is an Early Repressor of the CIITA MHC Class II Gene Expression during B Cell Differentiation to Plasma Cells
GEO Series GSE17999. Mus musculus. 4 samples. Type: Expression profiling by array.
Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses [Epigenetic CRISPRscreen]
GEO Series GSE189767. Homo sapiens. 6 samples. Type: Other.
PIKfyve inhibition upregulates surface expression of MHC class I to enhance immune responses in cancer
GEO Series GSE235945. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Data from: Contrasting evolutionary histories of MHC class I and class II loci in grouse - effects of selection and gene conversion
Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intra- and extra-cellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion played a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intra- and extra-cellular pathogens.
Data from: MHC class I diversity predicts non-random mating in Chinese alligators (Alligator sinensis)
The major histocompatibility complex (MHC) plays numerous important roles in kin recognition, pathogen resistance, and mate selection. Research in fish, birds, and mammals have suggested that individuals optimize MHC diversity, and therefore offspring fitness, when choosing mates. In reptiles, however, it is unclear whether female mate choice is based on genome-wide genetic characteristics such as microsatellites DNA loci, on particular functional trait loci (e.g., MHC) or on both, and MHC effects on mate choice remain relatively under-studied. Herein, we used 13 microsatellite loci and two MHC class I loci to investigate female mate choice of Chinese alligators (Alligator sinensis) in the semi-natural condition. We also determined correlations between the MHC genotype of breeding males and male reproductive success. We found that MHC-heterozygous males harbour a greater reproductive success, which possibly is the reason that those males were more preferred by the females than MHC-homozygous males. Furthermore, MHC class I amino-acid distance and functional distance of true mating pairs were higher compared with that of randomly sampled pairs. Analysis of microsatellites revealed that despite mate choice, individuals did not completely avoid inbreeding. These findings are the first evidence of MHC-associated mate choice in Chinese alligators, and they suggest that females may adopt different mating strategies after assessing MHC characteristics of potential mates.
Graph-pMHC: Graph Neural Network Approach to MHC Class II Peptide Presentation and Antibody Immunogenicity
<p>Antigen presentation on MHC Class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an anti-drug response. Significant progress has been made in pMHCII presentation modeling due to the collection of large-scale pMHC mass spectrometry datasets (ligandomes) and advances in machine learning. Here, we develop graph-pMHC, a graph neural network approach to predict pMHCII presentation. We derive adjacency matrices for pMHCII using Alphafold2-multimer, and address the peptide-MHC binding groove alignment problem with a simple graph enumeration strategy. We demonstrate that graph-pMHC dramatically outperforms methods with suboptimal inductive biases, such as the multilayer-perceptron-based NetMHCIIpan-4.0 (+20.17% absolute average precision). Finally, we create an antibody drug immunogenicity dataset from clinical trial data, and develop a method for measuring anti-antibody immunogenicity risk using pMHCII presentation models. Our model increases ROC AUC by 2.57% compared to just filtering peptides by hits in OASis alone for predicting antibody drug immunogenicity.<br><br>NOTE!!</p> <p>It's been brought to my attention that I accidentally shuffled the graph-pmhc and netmhciipan predictions on the antibody immunogenicity dataset (AB_df_w_preds), zenodo is not allowing me to add a new version. Besides these prediction columns the data is good, so the ada labels for the antibodies is fine. The graph-pmhc and netmhciipan predictions can be derived from AB_df_all_preds_w_preds with code like this:</p> <p>df.groupby('Antibody').apply(lambda x: sum((x['Peptide Num OAS Subjects']<23)&(x[column]>0))).values</p> <p>Where df is AB_df_all_preds_w_preds loaded in pandas, and column is the prediction column (graph-pmhc or netmhciipan) of interest. Sorry about the error!!</p>
Targeted demethylation and activation of NLRC5 augments cancer immunogenicity through MHC class I
GEO Series GSE233194. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Follicular lymphoma microenvironment characteristics associated with tumor cell mutations and MHC class II expression
GEO Series GSE203610. Homo sapiens. 67 samples. Type: Expression profiling by high throughput sequencing; Other.
Data from: Contrasting evolutionary histories of MHC class I and class II loci in grouse - effects of selection and gene conversion
Open the record for dataset details and reuse information.
Data from: MHC class I diversity predicts non-random mating in Chinese alligators (Alligator sinensis)
Open the record for dataset details and reuse information.
cIAP1/2 antagonism eliminates MHC class I negative tumors through T cell-dependent reprogramming of mononuclear phagocytes
GEO Series GSE150270. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides
GEO Series GSE48918. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer [RNA-Seq]
GEO Series GSE129381. Homo sapiens; Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.