Upload KnowledgeGraph/cluster_metrics_out/cluster_summaries.csv with huggingface_hub

KnowledgeGraph/cluster_metrics_out/cluster_summaries.csv

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+group_id,model_variant,n_nodes,top_gene_sets,top_pathways,top_go_terms,summary
+A0,GNN text-only,464,"GSE230450,GSE230520-2-vs-0-human up; GSE157785-0-vs-11-human dn; GSE133112-2-vs-1-human up; GSE180455-0-vs-5-human up; GSE117911-3-vs-5-human dn",Transcriptional regulation by RUNX3; Developmental Lineage of Pancreatic Ductal Cells; Regulation of CDH1 Function; Axon guidance; Degradation of the extracellular matrix; Nervous system development; PCP/CE pathway; Degradation of CDH1; Extracellular matrix organization; p53-Dependent G1 DNA Damage Response,Regulation Of Apoptotic Process; Regulation Of Cell Migration; Negative Regulation Of Programmed Cell Death; Positive Regulation Of DNA-templated Transcription; Regulation Of Cell Population Proliferation; Negative Regulation Of Apoptotic Process; Positive Regulation Of Cell Migration; Negative Regulation Of Cellular Process; Positive Regulation Of Intracellular Signal Transduction; Positive Regulation Of Transcription By RNA Polymerase II,"The gene set cluster is characterized by its association with the biological process of 'Negative Regulation Of Apoptotic Process'. This process involves the inhibition of programmed cell death, which is crucial for maintaining cellular homeostasis and preventing the development of diseases such as cancer. The genes in this cluster may play a role in regulating the balance between cell survival and death, which is essential for normal cellular function."
+A1,GNN text-only,499,"GSE163726-3-vs-4-human dn; GSE228991-3-vs-6-human up; GSE223548-5-vs-6-human up; GSE135640-2-vs-9-human dn; GSE201742,GSE201744-6-vs-3-human up",Developmental Lineage of Pancreatic Ductal Cells; Developmental Lineage of Mammary Gland Luminal Epithelial Cells; Transcriptional regulation by RUNX3; Degradation of the extracellular matrix; Extracellular matrix organization; Signaling by ALK in cancer; Nervous system development; Signaling by ALK fusions and activated point mutants; Collagen degradation; Axon guidance,Regulation Of Apoptotic Process; Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Positive Regulation Of Cell Migration; Positive Regulation Of Intracellular Signal Transduction; Negative Regulation Of Apoptotic Process; Negative Regulation Of Cellular Process; Negative Regulation Of Programmed Cell Death; Positive Regulation Of DNA-templated Transcription; Positive Regulation Of Cell Motility,"The gene sets in this cluster are primarily involved in the regulation of apoptosis, which is the programmed cell death process. These genes are crucial in maintaining cellular homeostasis and are implicated in various diseases, including cancer and immune disorders."
+A2,GNN text-only,410,"GSE137270,GSE160583-3-vs-6-human dn; GSE109143-2-vs-3-human dn; GSE218585-5-vs-9-human up; GSE223806,GSE223809-2-vs-4-human up; GSE154577-10-vs-12-human up",Metabolism of proteins; Metabolism of RNA; Translation; rRNA processing; FASTK family proteins regulate processing and stability of mitochondrial RNAs; tRNA processing in the mitochondrion; Signal Transduction; Mitochondrial RNA degradation; Cellular responses to stimuli; Mitochondrial translation,Macromolecule Biosynthetic Process; Peptide Biosynthetic Process; Translation; Cytoplasmic Translation; Gene Expression; Positive Regulation Of Cellular Biosynthetic Process; Ribonucleoprotein Complex Biogenesis; Ribosome Biogenesis; protein-RNA Complex Assembly; Ribosomal Small Subunit Biogenesis,"The gene set cluster is primarily associated with the biological process of translation, which involves the synthesis of proteins from RNA templates. This is evident from the frequent occurrence of pathways and terms related to translation and protein synthesis in the cluster."
+A3,GNN text-only,423,GSE234397-2-vs-1-human up; GSE152517-4-vs-11-human up; GSE53635-2-vs-3-human up; GSE158144-6-vs-5-human up; GSE163556-1-vs-0-human dn,Axon guidance; Nervous system development; Cellular responses to stimuli; Transcriptional regulation by RUNX3; Regulation of CDH1 Function; Assembly of the pre-replicative complex; PCP/CE pathway; Cellular responses to stress; Cell Cycle Checkpoints; Signaling by ALK fusions and activated point mutants,Regulation Of Apoptotic Process; Negative Regulation Of Programmed Cell Death; Negative Regulation Of Apoptotic Process; Positive Regulation Of DNA-templated Transcription; Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Regulation Of Translation; Ribonucleoprotein Complex Biogenesis; Ribosome Biogenesis; Positive Regulation Of Cell Population Proliferation,"The cluster of 423 gene sets is primarily related to the biological process of cell proliferation. These gene sets are associated with the regulation of cell population proliferation, translation, and transcription, as well as the assembly of the pre-replicative complex."
+A4,GNN text-only,344,"GSE255896-7-vs-6-human up; GSE148234-0-vs-2-human up; GSE199349-2-vs-12-human dn; GSE131473-2-vs-4-human up; GSE128634,GSE128636-4-vs-3-human up",Transcriptional regulation by RUNX3; Axon guidance; Nervous system development; Developmental Lineage of Pancreatic Ductal Cells; Signaling by ALK fusions and activated point mutants; Signaling by ALK in cancer; Extracellular matrix organization; NF-kB is activated and signals survival; p75NTR signals via NF-kB; Degradation of the extracellular matrix,Regulation Of Apoptotic Process; Regulation Of Cell Migration; Positive Regulation Of DNA-templated Transcription; Negative Regulation Of Apoptotic Process; Negative Regulation Of Programmed Cell Death; Positive Regulation Of Intracellular Signal Transduction; Regulation Of Cell Population Proliferation; Positive Regulation Of Transcription By RNA Polymerase II; Positive Regulation Of Cell Motility; Positive Regulation Of Apoptotic Process,"The gene set cluster is characterized by its involvement in the regulation of apoptotic processes and the positive regulation of transcription by RNA Polymerase II. These gene sets are likely to be related to cellular proliferation, differentiation, and response to stimuli."
+A5,GNN text-only,407,GSE158144-13-vs-5-human up; GSE213142-5-vs-0-human dn; GSE79888-3-vs-4-human up; GSE130534-9-vs-10-human up; GSE132913-4-vs-3-human dn,Cellular responses to stimuli; rRNA processing; Cellular responses to stress; Translation; Axon guidance; Nervous system development; Metabolism of RNA; Regulation of expression of SLITs and ROBOs; Metabolism of proteins; Response of EIF2AK4 (GCN2) to amino acid deficiency,Regulation Of Apoptotic Process; Positive Regulation Of Intracellular Signal Transduction; Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Negative Regulation Of Apoptotic Process; Translation; Gene Expression; Macromolecule Biosynthetic Process; Cytoplasmic Translation; Negative Regulation Of Programmed Cell Death,"The gene set cluster is primarily associated with the biological process of translation, which involves the synthesis of proteins from mRNA. This is supported by the high frequency of pathways and terms related to translation and protein metabolism."
+A6,GNN text-only,498,"GSE78102,GSE78110-2-vs-4-human dn; GSE247721,GSE247722-4-vs-6-human up; GSE152714-5-vs-6-human dn; GSE132624-5-vs-10-human dn; GSE131249-3-vs-4-human up",Developmental Lineage of Pancreatic Ductal Cells; Developmental Lineage of Mammary Gland Myoepithelial Cells; Nervous system development; Axon guidance; Degradation of the extracellular matrix; Extracellular matrix organization; Transcriptional regulation by RUNX3; Developmental Lineage of Mammary Gland Luminal Epithelial Cells; Integrin cell surface interactions; Interleukin-4 and Interleukin-13 signaling,Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Positive Regulation Of Intracellular Signal Transduction; Regulation Of Apoptotic Process; Positive Regulation Of Cell Migration; Positive Regulation Of Cell Motility; Positive Regulation Of Cell Population Proliferation; Negative Regulation Of Cell Population Proliferation; Regulation Of Intracellular Signal Transduction; Positive Regulation Of Cell Differentiation,"The gene sets in this cluster are primarily involved in the regulation of cell migration, proliferation, and differentiation. These processes are crucial for the development and maintenance of tissues and organs. The cluster may provide insights into the biological mechanisms underlying diseases where these processes are dysregulated."
+A7,GNN text-only,474,"GSE174745-1-vs-6-human dn; GSE174745-1-vs-4-human dn; GSE184875,GSE184877-3-vs-6-human dn; GSE186459-4-vs-6-human dn; GSE131300-5-vs-2-human dn",Developmental Lineage of Pancreatic Ductal Cells; Developmental Lineage of Mammary Gland Myoepithelial Cells; Nervous system development; Axon guidance; Non-integrin membrane-ECM interactions; Degradation of the extracellular matrix; Regulation of PD-L1(CD274) transcription; Senescence-Associated Secretory Phenotype (SASP); ECM proteoglycans; Developmental Cell Lineages of the Exocrine Pancreas,Regulation Of Cell Migration; Regulation Of Apoptotic Process; Positive Regulation Of DNA-templated Transcription; Positive Regulation Of Cell Migration; Negative Regulation Of Apoptotic Process; Macromolecule Biosynthetic Process; Regulation Of Cell Population Proliferation; Positive Regulation Of Intracellular Signal Transduction; Translation; Gene Expression,"The cluster of gene sets is primarily related to the development and function of the nervous system, particularly regarding axon guidance and the modulation of macrophage function in tumor microenvironments."
+A8,GNN text-only,261,"GSE58608,GSE60591-1-vs-6-human up; GSE149541,GSE149543-2-vs-3-human up; GSE61476-1-vs-2-human dn; GSE244307-1-vs-3-human dn; GSE109635-2-vs-1-human up",Translation; Major pathway of rRNA processing in the nucleolus and cytosol; rRNA processing in the nucleus and cytosol; rRNA processing; Metabolism of RNA; Metabolism of proteins; Translation initiation complex formation; Formation of a pool of free 40S subunits; GTP hydrolysis and joining of the 60S ribosomal subunit; L13a-mediated translational silencing of Ceruloplasmin expression,Histone Lysine Demethylation; Postsynaptic Membrane Assembly; Presynaptic Membrane Assembly; Postsynapse Assembly; Presynaptic Membrane Organization; Presynapse Organization; Sequestering Of Actin Monomers; Regulation Of Actin Filament Length; Neuron Cell-Cell Adhesion; Presynapse Assembly,"The gene sets in this cluster are related to the study of skeletal muscle transcriptomes, focusing on the amount of RNA sequencing data available and providing information on the baseline skeletal muscle transcriptome, including novel protein-coding transcripts."
+A9,GNN text-only,518,GSE187784-15-vs-11-human dn; GSE185192-9-vs-2-human up; GSE85443-7-vs-6-human dn; GSE133527-2-vs-0-human dn; GSE149353-6-vs-9-human up,Axon guidance; Nervous system development; Transcriptional regulation by RUNX3; Cellular responses to stimuli; Degradation of the extracellular matrix; Non-integrin membrane-ECM interactions; Cellular responses to stress; Extracellular matrix organization; Developmental Lineage of Pancreatic Ductal Cells; Fibronectin matrix formation,Regulation Of Cell Migration; Regulation Of Apoptotic Process; Positive Regulation Of Cell Migration; Positive Regulation Of DNA-templated Transcription; Negative Regulation Of Apoptotic Process; Negative Regulation Of Programmed Cell Death; Gene Expression; Regulation Of Cell Population Proliferation; Translation; Ribosome Biogenesis,"The gene set cluster is characterized by its role in the development of the nervous system in humans. The genes within this cluster are involved in various processes such as axon guidance, nervous system development, and transcriptional regulation, which are crucial for the proper formation and function of the nervous system."
+B0,GNN-beta structlite,437,"GSE161061-4-vs-3-human up; GSE218585-1-vs-5-human up; GSE247717,GSE247722-5-vs-3-human dn; GSE231324-7-vs-2-human up; GSE118947-7-vs-8-human up",Immune System; Metabolism of proteins; Cellular responses to stimuli; Cellular responses to stress; Developmental Biology; Cytokine Signaling in Immune system; Nervous system development; Signal Transduction; Disease; Axon guidance,Cellular Response To Cytokine Stimulus; Positive Regulation Of Intracellular Signal Transduction; Cytokine-Mediated Signaling Pathway; Cytoplasmic Translation; Positive Regulation Of Type I Interferon Production; Apoptotic Process; Peptide Biosynthetic Process; Response To Type II Interferon; Regulation Of Apoptotic Process; Defense Response To Symbiont,"The gene sets in this cluster are primarily involved in the immune system, with a focus on cytokine signaling and response to stress."
+B1,GNN-beta structlite,673,"GSE188392-0-vs-3-human dn; GSE157371-0-vs-2-human dn; GSE97619-4-vs-7-human dn; GSE97440,GSE97442-2-vs-3-human up; GSE149566-3-vs-10-human dn",Developmental Lineage of Pancreatic Ductal Cells; Transcriptional regulation by RUNX3; Degradation of the extracellular matrix; Axon guidance; Developmental Lineage of Mammary Gland Myoepithelial Cells; Nervous system development; RAC3 GTPase cycle; Extracellular matrix organization; Non-integrin membrane-ECM interactions; Assembly of the pre-replicative complex,Regulation Of Apoptotic Process; Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Positive Regulation Of Intracellular Signal Transduction; Positive Regulation Of Cell Migration; Negative Regulation Of Apoptotic Process; Positive Regulation Of DNA-templated Transcription; Negative Regulation Of Programmed Cell Death; Negative Regulation Of Cellular Process; Positive Regulation Of Cell Motility,"The cluster of 673 gene sets is primarily related to the regulation of apoptotic process, cell migration, cell population proliferation, and intracellular signal transduction. These processes are crucial for various developmental and disease contexts, highlighting the potential for further analysis and interpretation."
+B2,GNN-beta structlite,506,"GSE246602-4-vs-2-human up; GSE162165-2-vs-3-human dn; GSE109143-0-vs-1-human up; GSE160304,GSE163392-4-vs-1-human up; GSE114284-1-vs-5-human dn",Transcriptional regulation by RUNX3; Axon guidance; Nervous system development; PCP/CE pathway; Regulation of CDH1 Function; Cellular responses to stimuli; Assembly of the pre-replicative complex; Cell Cycle Checkpoints; Developmental Lineage of Pancreatic Ductal Cells; Asymmetric localization of PCP proteins,Regulation Of Apoptotic Process; Negative Regulation Of Programmed Cell Death; Regulation Of Cell Migration; Negative Regulation Of Apoptotic Process; Positive Regulation Of DNA-templated Transcription; Positive Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Positive Regulation Of Intracellular Signal Transduction; Regulation Of Translation; Positive Regulation Of Cell Motility,"The gene sets in this cluster are primarily related to the regulation of apoptotic processes. These genes are involved in the control of programmed cell death, which is a crucial mechanism in various biological processes and disease contexts."
+B3,GNN-beta structlite,494,GSE181158-7-vs-2-human up; GSE184029-7-vs-8-human dn; GSE173553-3-vs-2-human up; GSE210178-4-vs-2-human up; GSE108464-10-vs-14-human up,Axon guidance; Nervous system development; Non-integrin membrane-ECM interactions; ECM proteoglycans; Developmental Lineage of Pancreatic Ductal Cells; Degradation of the extracellular matrix; Collagen degradation; Extracellular matrix organization; Syndecan interactions; Integrin cell surface interactions,Regulation Of Cell Migration; Regulation Of Apoptotic Process; Positive Regulation Of Cell Migration; Negative Regulation Of Apoptotic Process; Regulation Of Cell Population Proliferation; Positive Regulation Of DNA-templated Transcription; Negative Regulation Of Programmed Cell Death; Positive Regulation Of Intracellular Signal Transduction; Positive Regulation Of Transcription By RNA Polymerase II; Positive Regulation Of Cell Motility,"The gene sets in this cluster are primarily related to the regulation of cell migration and proliferation, particularly in the context of steroidogenesis, proteasome inhibition, neutrophil hypersegmentation, and pancreatic ductal cell development."
+B4,GNN-beta structlite,172,"GSE137270,GSE160583-3-vs-6-human dn; GSE80062-0-vs-1-human up; GSE109143-2-vs-3-human dn; GSE229232-2-vs-4-human up; GSE113655-0-vs-6-human dn",Metabolism of proteins; Metabolism of RNA; Translation; rRNA processing; tRNA processing; FASTK family proteins regulate processing and stability of mitochondrial RNAs; Mitochondrial RNA degradation; tRNA processing in the mitochondrion; rRNA processing in the mitochondrion; Mitochondrial translation termination,Peptide Biosynthetic Process; Macromolecule Biosynthetic Process; Translation; Positive Regulation By Host Of Viral Process; Modulation By Host Of Viral Genome Replication; Gene Expression; Regulation Of Chaperone-Mediated Autophagy; Cellular Response To Epidermal Growth Factor Stimulus; Cytoplasmic Translation; Positive Regulation Of Cellular Biosynthetic Process,"The cluster of 172 gene sets is primarily related to the process of translation, which involves the synthesis of proteins from mRNA. This includes the metabolism of proteins and RNA, as well as the regulation of cellular biosynthetic processes. The gene sets are derived from various contexts such as cancer, immune response, and cellular response to stimuli."
+B5,GNN-beta structlite,289,"GSE231324-2-vs-0-human dn; GSE206391-1-vs-7-human up; GSE138712-1-vs-2-human dn; GSE192959,GSE193084-8-vs-3-human up; GSE119968-1-vs-4-human up",Metabolism of proteins; Metabolism of RNA; rRNA processing; Translation; Cellular responses to stimuli; Cellular responses to stress; Metabolism; Developmental Biology; Disease; Infectious disease,Histone Lysine Demethylation; Macromolecule Biosynthetic Process; Peptide Biosynthetic Process; Postsynaptic Membrane Assembly; Sequestering Of Actin Monomers; Presynaptic Membrane Assembly; Postsynapse Assembly; Presynaptic Membrane Organization; Regulation Of Actin Filament Length; Gene Expression,"The gene sets in this cluster are primarily related to the cellular response to stress and disease. These are characterized by the upregulation of genes involved in the immune response, inflammation, and cellular stress pathways."
+B6,GNN-beta structlite,822,"GSE230450,GSE230520-2-vs-0-human up; GSE108406-3-vs-7-human dn; GSE152497-11-vs-12-human up; GSE135640-6-vs-10-human up; GSE126776-2-vs-1-human up",Transcriptional regulation by RUNX3; Nervous system development; Developmental Lineage of Pancreatic Ductal Cells; Axon guidance; Degradation of the extracellular matrix; Signaling by ALK fusions and activated point mutants; Signaling by ALK in cancer; Regulation of CDH1 Function; Assembly of the pre-replicative complex; Extracellular matrix organization,Regulation Of Apoptotic Process; Regulation Of Cell Migration; Negative Regulation Of Apoptotic Process; Negative Regulation Of Programmed Cell Death; Regulation Of Cell Population Proliferation; Positive Regulation Of DNA-templated Transcription; Positive Regulation Of Cell Migration; Positive Regulation Of Intracellular Signal Transduction; Positive Regulation Of Cell Motility; Positive Regulation Of Cellular Process,"The gene sets in this cluster are primarily involved in the regulation of apoptotic processes. This includes the negative regulation of apoptotic process and negative regulation of programmed cell death, which are crucial for controlling cell death in various biological contexts."
+B7,GNN-beta structlite,421,GSE163726-3-vs-4-human dn; GSE143441-4-vs-11-human up; GSE140997-2-vs-1-human up; GSE157390-2-vs-3-human dn; GSE49321-8-vs-9-human up,Regulation of PD-L1(CD274) transcription; Developmental Lineage of Pancreatic Ductal Cells; Senescence-Associated Secretory Phenotype (SASP); Transcriptional regulation of granulopoiesis; Developmental Lineage of Mammary Gland Myoepithelial Cells; Amyloid fiber formation; IKK complex recruitment mediated by RIP1; Developmental Lineage of Mammary Gland Luminal Epithelial Cells; Fibronectin matrix formation; RNA Polymerase I Promoter Opening,Regulation Of Cell Migration; Regulation Of Apoptotic Process; Positive Regulation Of Intracellular Signal Transduction; Macromolecule Biosynthetic Process; Translation; Peptide Biosynthetic Process; Regulation Of Cell Population Proliferation; Cytoplasmic Translation; Gene Expression; Positive Regulation Of Cell Migration,"The gene set cluster is characterized by its focus on the immune system and how cells of the immune system, such as macrophages, alter their inflammatory profile depending on their microenvironment. This is particularly relevant in cancer and activated immune cells, where mechanisms like alternative polyadenylation in the 3'UTR (3'UTR-APA) and intronic polyadenylation (IPA) play a role in modulating gene expression."
+B8,GNN-beta structlite,33,"GSE150283-9-vs-5-human up; GSE158374-1-vs-3-human dn; GSE118947-2-vs-8-human dn; GSE204956-0-vs-3-human dn; GSE66207,GSE66209-2-vs-7-human dn","rRNA processing; Translation; Metabolism of RNA; Metabolism of proteins; Formation of the ternary complex, and subsequently, the 43S complex; Translation initiation complex formation; Ribosomal scanning and start codon recognition; Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S; Formation of a pool of free 40S subunits; GTP hydrolysis and joining of the 60S ribosomal subunit",Regulation Of Intracellular Steroid Hormone Receptor Signaling Pathway; Regulation Of Androgen Receptor Signaling Pathway; Histone Lysine Demethylation; Sequestering Of Actin Monomers; Regulation Of Actin Filament Length; Regulation Of Actin Filament Organization; Negative Regulation Of Actin Filament Polymerization; Regulation Of Actin Polymerization Or Depolymerization; Postsynaptic Membrane Assembly; Presynaptic Membrane Assembly,"The gene sets in this cluster are primarily associated with the regulation of actin filament length and organization. These processes are crucial for cell motility, cytoskeletal remodeling, and cell structure maintenance. Actin filaments, composed of actin monomers, are dynamic structures that play a key role in various cellular functions. The regulation of actin filament length is essential for the proper assembly and disassembly of actin filaments, which is critical for cell processes such as cell division, migration, and intracellular transport."
+B9,GNN-beta structlite,451,"GSE214558,GSE214559-3-vs-10-human dn; GSE176520-2-vs-5-human dn; GSE181600-0-vs-1-human dn; GSE201315-1-vs-9-human up; GSE205853-0-vs-2-human up",Transcriptional regulation by RUNX3; Axon guidance; Nervous system development; Signaling by ALK fusions and activated point mutants; Signaling by ALK in cancer; Integrin cell surface interactions; Extracellular matrix organization; Non-integrin membrane-ECM interactions; Degradation of the extracellular matrix; Interleukin-4 and Interleukin-13 signaling,Regulation Of Apoptotic Process; Regulation Of Cell Migration; Regulation Of Cell Population Proliferation; Positive Regulation Of DNA-templated Transcription; Positive Regulation Of Intracellular Signal Transduction; Negative Regulation Of Apoptotic Process; Positive Regulation Of Apoptotic Process; Negative Regulation Of Programmed Cell Death; Negative Regulation Of Cellular Process; Positive Regulation Of Cell Migration,"The cluster of 451 gene sets is primarily related to the biological process of transcriptional regulation, particularly in the context of beta cell survival in type 1 diabetes."