cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7034279.v1
title: Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of <i>Mycobacterium tuberculosis</i>

description: The ability of <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying <i>M. tb</i> persistence, how the bacteria achieve this goal is largely unknown. <i>Rv0081</i>, a member of the DosR regulon, is induced at the early stage of hypoxia while <i>Rv3334</i> is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of Δ<i>Rv0081</i> and Δ<i>Rv3334</i> revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of <i>Rv3334</i> while Rv3334 repressed transcription of <i>Rv0081</i>. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of <i>Rv3334</i>. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of <i>M. tb</i> to hypoxia.
DOI: 10.6084/m9.figshare.7558922
title: Additional file 2: of A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

description: Table S2. Different filtering criteria for raw sequences of RNA-seq data with different spot lengths (AvgSpotLen). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7558922.v1
title: Additional file 2: of A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

description: Table S2. Different filtering criteria for raw sequences of RNA-seq data with different spot lengths (AvgSpotLen). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7558937
title: Additional file 4: of A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

description: Table S3. SNVs detected by mapping RNA-seq of 19 barley accessions against either Morex HCâ +â LC or CWA. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.13323752.v1
title: Additional file 7 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 7. Subcluster 2 GO enrichment. Gene ontology enrichment of subcluster 2 as determined by k-means clustering
DOI: 10.6084/m9.figshare.13323731
title: Additional file 12 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 12. Gene expression evaluation by RT-qPCR. The expression pattern of all the selected genes in embryogenic cells (EC) vs. non-embryogenic cells (NEC) confirmed the RNAseq results.
DOI: 10.6084/m9.figshare.7559210.v1
title: Additional file 3: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Health to Disease Network in GML format. (GML 42 kb)
DOI: 10.6084/m9.figshare.13323734
title: Additional file 1 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 1. Differential gene expression profiles of NEC vs. EC in Jin668. Differentially expressed genes with functional annotations. The logFC value is the observed result in EC.
DOI: 10.6084/m9.figshare.13323740.v1
title: Additional file 3 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 3. Gene Ontology enrichment of genes upregulated in EC (&gt;=1 fold change). Gene ontology classification results of genes that are upregulated at least 1FC in embryogenic callus when compared to nonembryogenic callus.
DOI: 10.6084/m9.figshare.13323758.v1
title: Additional file 9 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 9. Phytohormone genes expressed in NEC and EC cells in Jin668. A list of all phytohormone annotated genes in the v2.0 of Gossypium hirsutum reference assembly with logFC values in EC.
DOI: 10.6084/m9.figshare.12277967
title: Equation_Normal.m represents the normal condition without the introduction of MM cells.; Equation_Normal.m, Equation_Tumor1.m, Equation_Tumor2.m, Equation_Tumor3.m and parameters.m are subfunctions. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.12277967.v1
title: Equation_Normal.m represents the normal condition without the introduction of MM cells.; Equation_Normal.m, Equation_Tumor1.m, Equation_Tumor2.m, Equation_Tumor3.m and parameters.m are subfunctions. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.13323749.v1
title: Additional file 6 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 6. Subcluster 1 GO enrichment. Gene ontology enrichment of subcluster 1 as determined by k-means clustering
DOI: 10.6084/m9.figshare.13323734.v1
title: Additional file 1 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 1. Differential gene expression profiles of NEC vs. EC in Jin668. Differentially expressed genes with functional annotations. The logFC value is the observed result in EC.
DOI: 10.6084/m9.figshare.13323746.v1
title: Additional file 5 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 5. Centered log2(fpkm+1) gene expression clusters of NEC and EC callus. Gene expression profiles of quantile normalized FPKM values for genes that were clustered by k-means clustering in NEC and EC callus.
DOI: 10.6084/m9.figshare.7559177
title: Additional file 13: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Parameters of the random networks generated with the null model in XLSX format. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.12277976.v1
title: Equation_Tumor3.m represents the condition in which the activation rate of IKK is inhibited after the introduction of MM cells. from Mathematical modelling of the role of GADD45<i>β</i> in the pathogenesis of multiple myeloma

description: Multiple myeloma (MM) is an incurable disease with relatively high morbidity and mortality rates. Great efforts were made to develop nuclear factor-kappa B (NF-κB)-targeted therapies against MM disease. However, these treatments influence MM cells as well as normal cells, inevitably causing serious side effects. Further research showed that NF-κB signalling promotes the survival of MM cells by interacting with JNK signalling through growth arrest and DNA damage-inducible beta (GADD45β), the downstream module of NF-κB signalling. The GADD45β-targeted intervention was suggested to be an effective and MM cell-specific treatment. However, the underlying mechanism through which GADD45β promotes the survival of MM cells is usually ignored in the previous models. A mathematical model of MM is built in this paper to investigate how NF-κB signalling acts along with JNK signalling through GADD45β and MKK7 to promote the survival of MM cells. The model cannot only mimic the variations in bone cells, the bone volume and MM cells with time, but it can also examine how the NF-κB pathway acts with the JNK pathway to promote the development of MM cells. In addition, the model also investigates the efficacies of GADD45β<i>-</i> and NF-κB-targeted treatments, suggesting that GADD45β-targeted therapy is more effective but has no apparent side effects. The simulation results match the experimental observations. It is anticipated that this model could be employed as a useful tool to initially investigate and even explore potential therapies involving the NF-κB and JNK pathways in the future.
DOI: 10.6084/m9.figshare.13323737
title: Additional file 2 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 2. Genes uniquely expressed in either NEC or EC cells. Genes with unique expression profiles in embryogenic or nonembryogenic callus with functional annotation from the definition line of Gossypium hirsutum v2.0 and Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.7559219.v1
title: Additional file 4: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Disease to Treatment Network in GML format. (GML 30 kb)
DOI: 10.6084/m9.figshare.13323755.v1
title: Additional file 8 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 8. Subcluster 3 GO enrichment. Gene ontology enrichment of subcluster 3 as determined by k-means clustering
DOI: 10.6084/m9.figshare.13323737.v1
title: Additional file 2 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 2. Genes uniquely expressed in either NEC or EC cells. Genes with unique expression profiles in embryogenic or nonembryogenic callus with functional annotation from the definition line of Gossypium hirsutum v2.0 and Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.13323743.v1
title: Additional file 4 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 4. Gene Ontology enrichment of genes downregulated EC (&gt;=1 fold change). Gene ontology classification results of genes that are downregulated at least 1FC in embryogenic callus when compared to nonembryogenic callus.
DOI: 10.15156/bio/sh1231437.09fu
title: SH1231437.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231438.09fu
title: SH1231438.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231439.09fu
title: SH1231439.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231440.09fu
title: SH1231440.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231441.09fu
title: SH1231441.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231442.09fu
title: SH1231442.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231443.09fu
title: SH1231443.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1231444.09fu
title: SH1231444.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.