Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0968 mdh

malate dehydrogenase (RefSeq)

CircVis
Functional Annotations (14)
Function System
Malate/lactate dehydrogenases cog/ cog
glycolysis go/ biological_process
malate metabolic process go/ biological_process
L-malate dehydrogenase activity go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Carbon fixation in photosynthetic organisms kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
MalateDH_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0968
(Mouseover regulator name to see its description)

RSP_0968 is regulated by 24 influences and regulates 0 modules.
Regulators for RSP_0968 mdh (24)
Regulator Module Operator
RSP_0394 166 tf
RSP_0395 166 tf
RSP_0698 166 tf
RSP_0755 166 tf
RSP_1163 166 tf
RSP_1231 166 tf
RSP_1704 166 tf
RSP_1739 166 tf
RSP_2494 166 tf
RSP_2730 166 tf
RSP_2850 166 tf
RSP_2889 166 tf
RSP_2922 166 tf
RSP_0327 25 tf
RSP_0698 25 tf
RSP_0728 25 tf
RSP_0755 25 tf
RSP_0927 25 tf
RSP_1231 25 tf
RSP_2610 25 tf
RSP_2867 25 tf
RSP_3202 25 tf
RSP_3203 25 tf
RSP_3464 25 tf

Warning: RSP_0968 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7770 7.30e+02 aAcGGtcAAgaacCa
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7771 4.50e+01 AcTtaaGgcGCtTcGCagaagcAt
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8052 4.30e+00 TTtccCGC
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8053 4.70e+02 AATTCAGACCTTTTCCTGA
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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 RSP_0968

RSP_0968 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
Malate/lactate dehydrogenases cog/ cog
glycolysis go/ biological_process
malate metabolic process go/ biological_process
L-malate dehydrogenase activity go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Carbon fixation in photosynthetic organisms kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
MalateDH_bact tigr/ tigrfam
Module neighborhood information for RSP_0968

RSP_0968 has total of 54 gene neighbors in modules 25, 166
Gene neighbors (54)
Gene Common Name Description Module membership
RSP_0005 guaA GMP synthase (glutamine-hydrolyzing) (NCBI) 166, 258
RSP_0147 glnA Glutamine synthetase class-I (NCBI) 25, 93
RSP_0250 RSP_0250 hypothetical protein (NCBI) 25, 278
RSP_0385 RSP_0385 Threonyl-tRNA synthetase, class IIa (NCBI) 166, 360
RSP_0404 RSP_0404 fructose - 1,6 - bisphosphatase, GlpX-like (NCBI) 166, 203
RSP_0550 RSP_0550 putative D-alanyl-D-alanine carboxypeptidase (NCBI) 25, 52
RSP_0745 RSP_0745 acetyl-CoA acetyltransferase (NCBI) 25, 195
RSP_0747 RSP_0747 Short-chain dehydrogenase/reductase (NCBI) 25, 195
RSP_0778 ProS Prolyl-tRNA synthetase, class IIa (NCBI) 166, 258
RSP_0815 aspS Aspartyl-tRNA synthetase (NCBI) 166, 248
RSP_0827 RSP_0827 Ribosomal protein L25 (NCBI) 104, 166
RSP_0832 RSP_0832 Putative GTP-binding protein (NCBI) 166, 192
RSP_0915 RSP_0915 hypothetical protein (NCBI) 25, 278
RSP_0943 yhxA probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI) 25, 175
RSP_0968 mdh malate dehydrogenase (RefSeq) 25, 166
RSP_1002 pyrB Aspartate/ornithine carbamoyltransferase (NCBI) 25, 224
RSP_1131 dapD 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI) 25, 192
RSP_1212 argG ArgG, Argininosuccinate synthase (NCBI) 109, 166
RSP_1342 dnaA chromosomal replication initiator protein, DnaA (NCBI) 25, 381
RSP_1343 RSP_1343 DNA polymerase III, beta chain (NCBI) 25, 372
RSP_1345 RSP_1345 hypothetical protein (NCBI) 25, 262
RSP_1376 asd putative aspartate-semialdehyde dehydrogenase (NCBI) 166, 192
RSP_1593 RSP_1593 NAD dependent malic enzyme (NCBI) 15, 25
RSP_1595 RSP_1595 Thymidine phosphorylase (NCBI) 15, 25
RSP_1598 RSP_1598 putative uracil phosphoribosyltransferase (NCBI) 15, 25
RSP_1613 RSP_1613 TRAP-T family transporter, DctP subunit (NCBI) 25, 291
RSP_1614 RSP_1614 TRAP-T family transporter with fused DctQ/DctM subunits (NCBI) 25, 112
RSP_1615 RSP_1615 hypothetical protein (NCBI) 25, 112
RSP_1761 pheT Phenylalanyl-tRNA synthetase beta chain (NCBI) 51, 166
RSP_1913 RSP_1913 3-oxoadipate CoA-transferase, beta subunit (NCBI) 25, 363
RSP_1914 RSP_1914 3-ketoacid CoA transferase alpha subunit (NCBI) 25, 363
RSP_1986 gatB Glutamyl-tRNA amidotransferase subunit B (NCBI) 25, 309
RSP_2088 lepA GTP-binding elongation factor (NCBI) 51, 166
RSP_2131 rne Ribonuclease E (NCBI) 25, 223
RSP_2307 RSP_2307 probable manganese-dependent inorganic pyrophosphatase (NCBI) 109, 166
RSP_2453 RSP_2453 putative oxidoreductase (NAD/NADP dependent) (NCBI) 71, 166
RSP_2461 fabG 3-oxoacyl-(acyl-carrier protein) reductase (NCBI) 166, 195
RSP_2465 RSP_2465 hypothetical protein (NCBI) 25, 203
RSP_2537 prfC Probable peptide chain release factor RF3 (NCBI) 72, 166
RSP_2622 ligA DNA ligase (NCBI) 25, 98
RSP_2697 RSP_2697 hypothetical protein (NCBI) 166, 184
RSP_2698 RSP_2698 putative quinoprotein (NCBI) 166, 240
RSP_2699 RSP_2699 Probable GTP-binding protein (NCBI) 166, 271
RSP_2737 RSP_2737 Putative ssRNA endoribonuclease L-PSP (NCBI) 166, 345
RSP_2781 RSP_2781 peroxiredoxin/glutaredoxin family protein (NCBI) 25, 184
RSP_2956 tktA Transketolase (NCBI) 166, 360
RSP_3349 RSP_3349 hypothetical protein (NCBI) 133, 166
RSP_4042 RSP_4042 Peptidyl-prolyl cis-trans isomerase, cyclophilin type (NCBI) 166, 345
RSP_4043 RSP_4043 Peptidylprolyl isomerase (NCBI) 162, 166
RSP_4044 pgk Phosphoglycerate kinase (NCBI) 166, 299
RSP_4045 fbaB Fructose-bisphosphate aldolase class I (NCBI) 166, 299
RSP_4047 pdhAa Pyruvate dehydrogenase E1 component, alpha subunit (NCBI) 25, 195
RSP_4049 pdhAb Pyruvate dehydrogenase E1 component, beta subunit (NCBI) 25, 291
RSP_4050 pdhB Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex (NCBI) 25, 291
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 RSP_0968
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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