Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/337143", "https://ndownloader.figshare.com/files/337177", "https://ndownloader.figshare.com/files/337278", "https://ndownloader.figshare.com/files/337312", "https://ndownloader.figshare.com/files/337360"], "description"=>"<div><h3>Background</h3><p>Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis.</p> <h3>Results</h3><p>We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality.</p> <h3>Conclusions</h3><p>CPNM provides a tool for biologists to explore PINs. It is freely accessible at <a href=\"http://www.biotextminer.com/CPNM/\">http://www.biotextminer.com/CPNM/</a>.</p> </div>", "links"=>[], "tags"=>["context-specific", "miner", "exploring", "networks"], "article_id"=>126631, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.s001", "https://dx.doi.org/10.1371/journal.pone.0034480.s002", "https://dx.doi.org/10.1371/journal.pone.0034480.s003", "https://dx.doi.org/10.1371/journal.pone.0034480.s004", "https://dx.doi.org/10.1371/journal.pone.0034480.s005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Context_Specific_Protein_Network_Miner_An_Online_System_for_Exploring_Context_Specific_Protein_Interaction_Networks_from_the_Literature/126631", "title"=>"Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-06 01:50:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/656819"], "description"=>"<p>Architecture of CPNM system.</p>", "links"=>[], "tags"=>["cpnm"], "article_id"=>327307, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Architecture_of_CPNM_system_/327307", "title"=>"Architecture of CPNM system.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/656937"], "description"=>"<p>CPNM web interface with query builder.</p>", "links"=>[], "tags"=>["interface", "query"], "article_id"=>327422, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CPNM_web_interface_with_query_builder_/327422", "title"=>"CPNM web interface with query builder.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:03:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/657059"], "description"=>"<p>Sample query formulation by CPNM.</p>", "links"=>[], "tags"=>["query", "formulation"], "article_id"=>327546, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_query_formulation_by_CPNM_/327546", "title"=>"Sample query formulation by CPNM.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:05:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/657225"], "description"=>"<p>CPNM output showing protein interactions extracted from literature for Case Study I.</p>", "links"=>[], "tags"=>["interactions", "extracted"], "article_id"=>327710, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CPNM_output_showing_protein_interactions_extracted_from_literature_for_Case_Study_I_/327710", "title"=>"CPNM output showing protein interactions extracted from literature for Case Study I.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:08:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/657321"], "description"=>"<p>PIN generated by CPNM for Case Study I.</p>", "links"=>[], "tags"=>["generated", "cpnm"], "article_id"=>327805, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PIN_generated_by_CPNM_for_Case_Study_I_/327805", "title"=>"PIN generated by CPNM for Case Study I.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:10:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/657434"], "description"=>"<p>PIN generated by CPNM for Case Study II.</p>", "links"=>[], "tags"=>["generated", "cpnm"], "article_id"=>327923, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PIN_generated_by_CPNM_for_Case_Study_II_/327923", "title"=>"PIN generated by CPNM for Case Study II.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:12:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/657563"], "description"=>"<p>Hub nodes in PIN generated by CPNM for Case Study II.</p>", "links"=>[], "tags"=>["nodes", "generated", "cpnm"], "article_id"=>328047, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hub_nodes_in_PIN_generated_by_CPNM_for_Case_Study_II_/328047", "title"=>"Hub nodes in PIN generated by CPNM for Case Study II.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-06 02:14:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/657662"], "description"=>"<p>Only links associated with hub-node proteins (refer <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034480#pone-0034480-t004\" target=\"_blank\">Table 4</a>) are shown.</p>", "links"=>[], "tags"=>["pairs", "shown", "nodes"], "article_id"=>328146, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evidence_edge_strength_between_network_protein_pairs_shown_in_Figure_5_more_links_edges_between_two_nodes_typically_would_mean_more_support_in_the_literature_/328146", "title"=>"Evidence (edge) strength between network protein pairs shown in Figure 5 (more links/edges between two nodes typically would mean more support in the literature).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:15:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/657694"], "description"=>"<p>This table shows that IL13, IL4, FLG, GRP, IL10, STAT6, and TSLP may be important hub-proteins in the network for the target biological context (IL13, asthma, human). Only nodes with two or more neighbours are shown.</p>", "links"=>[], "tags"=>["neighbour", "diagram"], "article_id"=>328182, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Node_neighbour_hub_protein_statistics_in_the_network_diagram_Figure_5_/328182", "title"=>"Node neighbour (hub-protein) statistics in the network diagram (Figure 5).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:16:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/657745"], "description"=>"<p>Highlighted in bold are the pathways that are known to be associated with asthma as per annotation provided in the source databases in hiPathDB.</p>", "links"=>[], "tags"=>["hub-node", "proteins", "generated", "cpnm", "pathway", "hipathdb"], "article_id"=>328216, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pathway_involvement_of_the_hub_node_proteins_in_the_context_specific_network_generated_by_CPNM_in_Case_Study_I_using_pathway_information_given_in_hiPathDB_database_61_/328216", "title"=>"Pathway involvement of the hub-node proteins in the context specific network generated by CPNM in Case Study I using pathway information given in hiPathDB database [61].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:16:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/657770"], "description"=>"<p>This table shows the distribution of direction information for a given protein in the network diagram shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034480#pone-0034480-g005\" target=\"_blank\">Figure 5</a>. Only links associated with hub-node proteins (refer <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034480#pone-0034480-t004\" target=\"_blank\">Table 4</a>) are shown.</p>", "links"=>[], "tags"=>["undirected", "connectivity"], "article_id"=>328255, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Outbound_inbound_and_undirected_edge_connectivity_for_a_node_/328255", "title"=>"Outbound, inbound, and undirected edge connectivity for a node.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:17:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/657806"], "description"=>"<p>Accuracy of CPNM on gene/protein name tagging task using holdout test datasets from AIMed and BioCreative.</p>", "links"=>[], "tags"=>["cpnm", "tagging", "holdout", "datasets", "aimed"], "article_id"=>328290, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_CPNM_on_gene_protein_name_tagging_task_using_holdout_test_datasets_from_AIMed_and_BioCreative_/328290", "title"=>"Accuracy of CPNM on gene/protein name tagging task using holdout test datasets from AIMed and BioCreative.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:18:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/657841"], "description"=>"<p>Accuracy of CPNM on PI directionality prediction task based on 10-fold cross validation on a gold-standard dataset.</p>", "links"=>[], "tags"=>["cpnm", "pi", "directionality", "10-fold", "validation", "gold-standard"], "article_id"=>328324, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_CPNM_on_PI_directionality_prediction_task_based_on_10_fold_cross_validation_on_a_gold_standard_dataset_/328324", "title"=>"Accuracy of CPNM on PI directionality prediction task based on 10-fold cross validation on a gold-standard dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:18:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/657876"], "description"=>"<p>Accuracy of CPNM on PI triplet prediction task based on 10-fold cross validation on a gold-standard dataset.</p>", "links"=>[], "tags"=>["cpnm", "pi", "triplet", "10-fold", "validation", "gold-standard"], "article_id"=>328357, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_CPNM_on_PI_triplet_prediction_task_based_on_10_fold_cross_validation_on_a_gold_standard_dataset_/328357", "title"=>"Accuracy of CPNM on PI triplet prediction task based on 10-fold cross validation on a gold-standard dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:19:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/657916"], "description"=>"<p>List of differentially expressed genes with fold change >3 selected for Case Study II.</p>", "links"=>[], "tags"=>["differentially", "genes"], "article_id"=>328402, "categories"=>["Biological Sciences"], "users"=>["Rajesh Chowdhary", "Sin Lam Tan", "Jinfeng Zhang", "Shreyas Karnik", "Vladimir B. Bajic", "Jun S. Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0034480.t008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_differentially_expressed_genes_with_fold_change_gt_3_selected_for_Case_Study_II_/328402", "title"=>"List of differentially expressed genes with fold change >3 selected for Case Study II.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-06 02:20:02"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Computer and information sciences", "average_usage"=>[352, 587, 696, 809, 901, 989, 1072, 1156, 1257, 1334, 1422, 1486, 1555, 1647, 1714, 1780, 1844, 1919, 1997, 2051, 2138, 2198, 2267, 2324, 2391]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[312, 547, 668, 769, 861, 953, 1046, 1135, 1224, 1307, 1388, 1464, 1536, 1606, 1676, 1744, 1812, 1882, 1954, 2020, 2089, 2155, 2218, 2282, 2344]}]}
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