cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14684715
title: Additional file 13 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 13: Table S8. Results table for the survival analysis of Uniprot keyword values. Description: Rows represent the features analyzed. Columns: feature is the Uniprot identifier, combined. PV is the sum of the negative logarithms in base 10 of the survival p-values in the three cancers, PV.[cancer] is the raw p-value of the survival analysis in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the survival analysis in cancer [cancer].
DOI: 10.6084/m9.figshare.14684715.v1
title: Additional file 13 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 13: Table S8. Results table for the survival analysis of Uniprot keyword values. Description: Rows represent the features analyzed. Columns: feature is the Uniprot identifier, combined. PV is the sum of the negative logarithms in base 10 of the survival p-values in the three cancers, PV.[cancer] is the raw p-value of the survival analysis in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the survival analysis in cancer [cancer].
DOI: 10.6084/m9.figshare.14684718
title: Additional file 14 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 14: Table S9. esults table for the comparison of normal versus tumor tissue of miRNA values. Description: Rows represent the features analyzed. Columns: feature is the miRNA identifier, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684718.v1
title: Additional file 14 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 14: Table S9. esults table for the comparison of normal versus tumor tissue of miRNA values. Description: Rows represent the features analyzed. Columns: feature is the miRNA identifier, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684709.v1
title: Additional file 11 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 11: Table S6. Results table for the survival analysis of path values. Description: Rows represent the features analyzed. Columns: feature is the Hipathia path identifier, combined. PV is the sum of the negative logarithms in base 10 of the survival p-values in the three cancers, PV.[cancer] is the raw p-value of the survival analysis in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the survival analysis in cancer [cancer].
DOI: 10.6084/m9.figshare.14684721.v1
title: Additional file 15 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 15: Table S10. Table of miRNA, gene and path relations. Description: Rows represent relations. Columns include: miRNA, the name of the miRNA, gene, the gene targeted by the miRNA, node, Hipathia code of the node including the gene, node.label, readable name of the node, path, Hipathia name of the path including the node, path.label, readable name of the path including the node, pathway, KEGG pathway code including the path, and pathway.label, name of the KEGG pathway including the path.
DOI: 10.6084/m9.figshare.14684721
title: Additional file 15 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 15: Table S10. Table of miRNA, gene and path relations. Description: Rows represent relations. Columns include: miRNA, the name of the miRNA, gene, the gene targeted by the miRNA, node, Hipathia code of the node including the gene, node.label, readable name of the node, path, Hipathia name of the path including the node, path.label, readable name of the path including the node, pathway, KEGG pathway code including the path, and pathway.label, name of the KEGG pathway including the path.
DOI: 10.6084/m9.figshare.14684712.v1
title: Additional file 12 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 12: Table S7. Results table for the survival analysis of GO term values. Description: Rows represent the features analyzed. Columns: feature is the GO identifier, combined. PV is the sum of the negative logarithms in base 10 of the survival p-values in the three cancers, PV.[cancer] is the raw p-value of the survival analysis in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the survival analysis in cancer [cancer].
DOI: 10.6084/m9.figshare.14684736
title: Additional file 5 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 5: Figure SF5. Survival analysis of cancer subtypes resulting from clustering by GO terms values. Description: A: Clustering of the tumor samples from BRCA, KIRC and LUAD based on the values of the GO terms which resulted significant in the comparison between healthy and tumor tissues in all three cancer types, colored by their tissue of origin (Tissue) and the subcluster in which they have been stratified. B: Kaplan-Meier curves of the subgroups created in each cancer, with the p-value of the survival analysis performed at the bottom. Curve colors are not matched with the subcluster colors but defined to be easily differentiated. Figure SF6. Survival analysis of cancer subtypes resulting from clustering by Uniprot function values. Description: A: Clustering of the tumor samples from BRCA, KIRC and LUAD based on the values of the Uniprot keywords which resulted significant in the comparison between healthy and tumor tissues in all three cancer types, colored by their tissue of origin (Tissue) and the subcluster in which they have been stratified. B: Kaplan-Meier curves of the subgroups created in each cancer, with the p-value of the survival analysis performed at the bottom. Curve colors are not matched with the subcluster colors but defined to be easily differentiated. Figure SF7. Specific functions per cancer and survival related to AMPK signaling pathway: CCNA2. Description: A) UpSet plot indicating the number of paths in the pairwise intersections among the three analyzed cancers, and the (null) intersection of the three of them. C) Kaplan-Meier curves for the three groups of activation intensity defined by path AMPK signaling pathway: CCNA2 in KIRC (top) and LUAD (bottom). Blue lines correspond to the 20% of samples with lowest activity values, red lines correspond to the 20% of samples with highest activity values of this pathway and orange lines correspond to the remaining 60% of samples.
DOI: 10.6084/m9.figshare.14684742
title: Additional file 7 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 7: Table S2. Results table for the comparison of normal versus tumor tissue of Gene Ontology (GO) term values. Description: Rows represent the features analyzed. Columns: feature is the GO identifier, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684736.v1
title: Additional file 5 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 5: Figure SF5. Survival analysis of cancer subtypes resulting from clustering by GO terms values. Description: A: Clustering of the tumor samples from BRCA, KIRC and LUAD based on the values of the GO terms which resulted significant in the comparison between healthy and tumor tissues in all three cancer types, colored by their tissue of origin (Tissue) and the subcluster in which they have been stratified. B: Kaplan-Meier curves of the subgroups created in each cancer, with the p-value of the survival analysis performed at the bottom. Curve colors are not matched with the subcluster colors but defined to be easily differentiated. Figure SF6. Survival analysis of cancer subtypes resulting from clustering by Uniprot function values. Description: A: Clustering of the tumor samples from BRCA, KIRC and LUAD based on the values of the Uniprot keywords which resulted significant in the comparison between healthy and tumor tissues in all three cancer types, colored by their tissue of origin (Tissue) and the subcluster in which they have been stratified. B: Kaplan-Meier curves of the subgroups created in each cancer, with the p-value of the survival analysis performed at the bottom. Curve colors are not matched with the subcluster colors but defined to be easily differentiated. Figure SF7. Specific functions per cancer and survival related to AMPK signaling pathway: CCNA2. Description: A) UpSet plot indicating the number of paths in the pairwise intersections among the three analyzed cancers, and the (null) intersection of the three of them. C) Kaplan-Meier curves for the three groups of activation intensity defined by path AMPK signaling pathway: CCNA2 in KIRC (top) and LUAD (bottom). Blue lines correspond to the 20% of samples with lowest activity values, red lines correspond to the 20% of samples with highest activity values of this pathway and orange lines correspond to the remaining 60% of samples.
DOI: 10.6084/m9.figshare.14684739.v1
title: Additional file 6 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 6: Table S1. Results table for the comparison of normal versus tumor tissue of path values. Description: Rows represent the features analyzed. Columns: feature is the Hipathia identifier, name is the human readable name, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684745
title: Additional file 8 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 8: Table S3. Results table for the comparison of normal versus tumor tissue of Uniprot keyword values. Description: Rows represent the features analyzed. Columns: feature is the Uniprot identifier, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684748
title: Additional file 9 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 9: Table S4. Metrics results from the algorithm comparison through K-Fold Cross-Validation to classify tumor and healthy tissue. Description: The comparison has been made by cancer type (BRCA, LUAD, KIRC), taking in account either all significant paths or only the top ten most significant ones. The algorithms used were K-Nearest-Neighbor (KNN), Decision Tree (CART), Naive-Bayes Classificator (NB), K-Means clustering (KMN) and Random Forest (RF). The metrics analysed take account of the mean Accuracy of the model testing across all the possible training and test combinations data splits resulting from the K-Fold Cross-Validation, along with its associated Standard Deviation.
DOI: 10.6084/m9.figshare.14684739
title: Additional file 6 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 6: Table S1. Results table for the comparison of normal versus tumor tissue of path values. Description: Rows represent the features analyzed. Columns: feature is the Hipathia identifier, name is the human readable name, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684745.v1
title: Additional file 8 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 8: Table S3. Results table for the comparison of normal versus tumor tissue of Uniprot keyword values. Description: Rows represent the features analyzed. Columns: feature is the Uniprot identifier, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684742.v1
title: Additional file 7 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 7: Table S2. Results table for the comparison of normal versus tumor tissue of Gene Ontology (GO) term values. Description: Rows represent the features analyzed. Columns: feature is the GO identifier, common is a boolean indicating whether the feature is significant in all three cancers, type indicates whether the feature is unidirectional, bidirectional or not common, subtype classifies common features into 8 subgroups (unidirectional can be ALL UP or ALL DOWN, indicating whether the feature has positive or negative statistic in all three cancers, respectively, and bidirectional are represented by the cancer that differs from the other two, so that KIRC UP represent the group of features which a positive statistic in KIRC and negative one in BRCA and LUAD), combined. PV is the sum of the negative logarithms in base 10 of the comparison p-values in the three cancers, sign.[cancer] is the direction of the change in cancer [cancer], stat.[cancer] is the statistic of the comparison in cancer [cancer] and adj. PV.[cancer] is the FDR adjusted p-value of the comparison in cancer [cancer].
DOI: 10.6084/m9.figshare.14684748.v1
title: Additional file 9 of Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers

description: Additional file 9: Table S4. Metrics results from the algorithm comparison through K-Fold Cross-Validation to classify tumor and healthy tissue. Description: The comparison has been made by cancer type (BRCA, LUAD, KIRC), taking in account either all significant paths or only the top ten most significant ones. The algorithms used were K-Nearest-Neighbor (KNN), Decision Tree (CART), Naive-Bayes Classificator (NB), K-Means clustering (KMN) and Random Forest (RF). The metrics analysed take account of the mean Accuracy of the model testing across all the possible training and test combinations data splits resulting from the K-Fold Cross-Validation, along with its associated Standard Deviation.
DOI: 10.6084/m9.figshare.14684763
title: Additional file 1 of PTMViz: a tool for analyzing and visualizing histone post translational modification data

description: Additional file 1. The data and PTMviz scripts.
DOI: 10.6084/m9.figshare.14684805
title: Additional file 4 of Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

description: Additional file 4: Table S1. Primer sequences used for expression analysis, cloning, subcellular localization, vector construction and transgenic confirmation.
DOI: 10.6084/m9.figshare.14684805.v1
title: Additional file 4 of Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

description: Additional file 4: Table S1. Primer sequences used for expression analysis, cloning, subcellular localization, vector construction and transgenic confirmation.
DOI: 10.6084/m9.figshare.14684808
title: Additional file 5 of Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

description: Additional file 5: Table S2. The cis-acting element analysis of PbrPUB gene family in pear.
DOI: 10.6084/m9.figshare.14684808.v1
title: Additional file 5 of Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

description: Additional file 5: Table S2. The cis-acting element analysis of PbrPUB gene family in pear.
DOI: 10.6084/m9.figshare.14684850
title: Additional file 2 of Investigating ADR mechanisms with Explainable AI: a feasibility study with knowledge graph mining

description: Additional file 2. This file includes the results of the manual evaluation performed by three experts about the explanatory character of predictive features.
DOI: 10.6084/m9.figshare.14684850.v1
title: Additional file 2 of Investigating ADR mechanisms with Explainable AI: a feasibility study with knowledge graph mining

description: Additional file 2. This file includes the results of the manual evaluation performed by three experts about the explanatory character of predictive features.
DOI: 10.6084/m9.figshare.14684863
title: Additional file 4 of A new KSRP-binding compound suppresses distant metastasis of colorectal cancer by targeting the oncogenic KITENIN complex

description: Additional file 4: Supplementary Figure 4. Differences in cell survival after treatment with 5-FU or oxaliplatin in the presence or absence of DKC1125 in CRC cells overexpressing KITENIN. Various CRC cells (CT-26, Caco2, HCT116, and HT29) were seeded at 5 × 103 cells/well on 96-well plates, and the cytotoxicity of the indicated concentrations of 5-fluorouracil (5-FU, 0.02, 0.1, 0.5 μg/ml, a-c) or oxaliplatin (oxa, 1, 3, 10 μM, d) combined with DKC1125 (#25, 0.5, 1.5, 4.5 μM) was examined by tetrazolium salt (WST-8) assay 72 h after seeding. Data shown in line graphs (mean ± SEM, n = 3) were compared among groups at three time points (24, 48, and 72 h). The optical density (O.D.) values of each time point (24, 48, 72 h) were recalculated using the criterion that the O.D. value of 24 h with no treatment (5-FU and DKC1125) is set to 1.0. The asterisk indicates a significant difference between the indicated groups at each time point (*P