Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_1501

D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (IMGterm)

CircVis
Functional Annotations (11)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
cysteine-type endopeptidase inhibitor activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
NAD binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PGDH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_1501
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_1501!

Warning: Synpcc7942_1501 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
1604 1.60e+03 aaCaGcagTCa
Loader icon
1605 3.00e+04 cgGGtTggggTgC.G
Loader icon
1606 5.00e+03 tggCC.gttTc
Loader icon
1910 1.10e+01 ATTCtCaaGtTaATttATccT.AA
Loader icon
1911 8.90e+03 CaGGCTGCT.cCA
Loader icon
1912 1.50e+04 TcTtcAtcagCccTcgGTCAg
Loader icon
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_1501

Synpcc7942_1501 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
cysteine-type endopeptidase inhibitor activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
NAD binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
PGDH tigr/ tigrfam
Module neighborhood information for Synpcc7942_1501

Synpcc7942_1501 has total of 40 gene neighbors in modules 28, 131
Gene neighbors (40)
Gene Common Name Description Module membership
Synpcc7942_0126 Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) (IMGterm) 74, 131
Synpcc7942_0178 ATPase 14, 131
Synpcc7942_0241 23S rRNA m(5)U-1939 methyltransferase (EC 2.1.1.-) (IMGterm) 73, 131
Synpcc7942_0434 hypothetical protein 14, 131
Synpcc7942_0449 seryl-tRNA synthetase (EC 6.1.1.11) (IMGterm) 74, 131
Synpcc7942_0733 "Phage portal protein, lambda" 28, 45
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_0788 glutathione S-transferase (EC:2.5.1.18) 36, 131
Synpcc7942_1026 fibronectin binding protein-like 36, 131
Synpcc7942_1190 leucyl aminopeptidase (EC:3.4.11.1). Metallo peptidase. MEROPS family M17 (IMGterm) 28, 46
Synpcc7942_1222 truB tRNA pseudouridine synthase B (EC 4.2.1.70) (IMGterm) 28, 179
Synpcc7942_1316 Mn transporter MntC 131, 169
Synpcc7942_1319 Uracil phosphoribosyltransferase (EC:2.4.2.9) 131, 169
Synpcc7942_1364 hypothetical protein 8, 131
Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (IMGterm) 28, 131
Synpcc7942_1503 RNA-binding S4 30, 131
Synpcc7942_1548 probable amidase 85, 131
Synpcc7942_1624 "riboflavin synthase, alpha subunit (EC:2.5.1.9)" 131, 154
Synpcc7942_1673 hypothetical protein 73, 131
Synpcc7942_1990 hypothetical protein 14, 131
Synpcc7942_2063 surE 5'-nucleotidase (EC 3.1.3.5) / exopolyphosphatase (EC 3.6.1.11) / 3'-nucleotidase (EC 3.1.3.6) (IMGterm) 74, 131
Synpcc7942_2213 adk Adenylate kinase (EC 2.7.4.3) (IMGterm) 28, 75
Synpcc7942_2219 rpsH SSU ribosomal protein S8P (IMGterm) 28, 119
Synpcc7942_2220 rplE LSU ribosomal protein L5P (IMGterm) 28, 119
Synpcc7942_2224 LSU ribosomal protein L29P (IMGterm) 28, 200
Synpcc7942_2271 ADP-ribose pyrophosphatase (EC:3.6.1.13) 8, 131
Synpcc7942_2470 hypothetical protein 74, 131
Synpcc7942_2539 hypothetical protein 36, 131
Synpcc7942_2576 hypothetical protein 88, 131
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_1501
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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