Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_0098

pyruvate kinase (EC 2.7.1.40) (IMGterm)

CircVis
Functional Annotations (14)
Function System
Pyruvate kinase cog/ cog
magnesium ion binding go/ molecular_function
pyruvate kinase activity go/ molecular_function
glycolysis go/ biological_process
phosphorylation go/ biological_process
potassium ion binding go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Purine metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Carbon fixation in photosynthetic organisms kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
pyruv_kin tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_0098
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_0098!

Warning: Synpcc7942_0098 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1535 1.30e+03 gGctgaTttgAcCA
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1536 6.70e+03 TtGgcTtTgCT
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1537 4.70e+04 t.AaTg.TgtCgacgTggtgG
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1745 4.50e+01 tgCATCAA
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1746 5.40e+03 C..GTCGaggTGctG
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1747 3.20e+04 T.TCTTTtCCA
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for Synpcc7942_0098

Synpcc7942_0098 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
Pyruvate kinase cog/ cog
magnesium ion binding go/ molecular_function
pyruvate kinase activity go/ molecular_function
glycolysis go/ biological_process
phosphorylation go/ biological_process
potassium ion binding go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Purine metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Carbon fixation in photosynthetic organisms kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
pyruv_kin tigr/ tigrfam
Module neighborhood information for Synpcc7942_0098

Synpcc7942_0098 has total of 54 gene neighbors in modules 5, 75
Gene neighbors (54)
Gene Common Name Description Module membership
Synpcc7942_0098 pyruvate kinase (EC 2.7.1.40) (IMGterm) 5, 75
Synpcc7942_0260 ATPase 5, 49
Synpcc7942_0347 hypothetical protein 5, 186
Synpcc7942_0514 hypothetical protein 5, 181
Synpcc7942_0561 hypothetical protein 4, 5
Synpcc7942_0685 groEL Chaperonin Cpn60/TCP-1 5, 35
Synpcc7942_0734 hypothetical protein 28, 75
Synpcc7942_0735 hypothetical protein 28, 75
Synpcc7942_0736 electron transfer protein 28, 75
Synpcc7942_0737 hypothetical protein 28, 75
Synpcc7942_0742 hypothetical protein 28, 75
Synpcc7942_0743 hypothetical protein 28, 75
Synpcc7942_0744 hypothetical protein 28, 75
Synpcc7942_0745 hypothetical protein 28, 75
Synpcc7942_0746 hypothetical protein 28, 75
Synpcc7942_0747 hypothetical protein 28, 75
Synpcc7942_0748 Phage major tail tube protein 28, 75
Synpcc7942_0750 "Phage tail tape measure protein TP901, core region" 28, 75
Synpcc7942_0884 translation elongation factor 1A (EF-1A/EF-Tu) (IMGterm) 75, 200
Synpcc7942_0885 translation elongation factor 2 (EF-2/EF-G) (IMGterm) 75, 200
Synpcc7942_1056 "transcriptional regulator, XRE family (IMGterm)" 5, 90
Synpcc7942_1059 hypothetical protein 5, 82
Synpcc7942_1443 fructose-bisphosphate aldolase (EC 4.1.2.13) (IMGterm) 5, 160
Synpcc7942_1524 DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) (IMGterm) 5, 43
Synpcc7942_1542 iron-stress chlorophyll-binding protein 5, 14
Synpcc7942_1683 hypothetical protein 5, 186
Synpcc7942_1684 "putative transcriptional regulator, Crp/Fnr family" 5, 186
Synpcc7942_1735 Iron-regulated ABC transporter membrane component SufB (IMGterm) 5, 117
Synpcc7942_1736 Iron-regulated ABC transporter ATPase subunit SufC (IMGterm) 5, 43
Synpcc7942_1737 Iron-regulated ABC transporter permease protein SufD (IMGterm) 5, 43
Synpcc7942_1738 cysteine desulfurase (EC 2.8.1.7) (IMGterm) 5, 43
Synpcc7942_1926 hypothetical protein 5, 183
Synpcc7942_2213 adk Adenylate kinase (EC 2.7.4.3) (IMGterm) 28, 75
Synpcc7942_2214 secY protein translocase subunit secY/sec61 alpha (IMGterm) 75, 195
Synpcc7942_2215 rplO LSU ribosomal protein L15P (IMGterm) 5, 195
Synpcc7942_2217 rplR LSU ribosomal protein L18P (IMGterm) 5, 119
Synpcc7942_2218 rplF LSU ribosomal protein L6P (IMGterm) 5, 119
Synpcc7942_2221 rplX LSU ribosomal protein L24P (IMGterm) 5, 119
Synpcc7942_2222 rplN LSU ribosomal protein L14P (IMGterm) 5, 119
Synpcc7942_2223 rpsQ SSU ribosomal protein S17P (IMGterm) 5, 119
Synpcc7942_2225 rplP LSU ribosomal protein L16P (IMGterm) 5, 119
Synpcc7942_2226 rpsC SSU ribosomal protein S3P (IMGterm) 5, 119
Synpcc7942_2229 rplB LSU ribosomal protein L2P (IMGterm) 75, 200
Synpcc7942_2230 rplW LSU ribosomal protein L23P (IMGterm) 75, 200
Synpcc7942_2231 rplD LSU ribosomal protein L4P (IMGterm) 75, 200
Synpcc7942_2232 rplC LSU ribosomal protein L3P (IMGterm) 75, 200
Synpcc7942_2287 hypothetical protein 5, 94
Synpcc7942_2314 groES "GroES protein, 10 kD chaperonin" 5, 114
Synpcc7942_2338 hypothetical protein 5, 12
Synpcc7942_2437 ileS Isoleucyl-tRNA synthetase (EC 6.1.1.5) (IMGterm) 5, 72
Synpcc7942_2440 Polyribonucleotide nucleotidyltransferase (EC:2.7.7.8) 5, 11
Synpcc7942_2530 rpsB SSU ribosomal protein S2P (IMGterm) 5, 200
Synpcc7942_2531 tsf translation elongation factor Ts (EF-Ts) (IMGterm) 75, 200
Synpcc7942_2533 hypothetical protein 5, 135
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for Synpcc7942_0098
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend