Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0962

Dihydrolipoamide dehydrogenase (NCBI)

CircVis
Functional Annotations (16)
Function System
Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes cog/ cog
dihydrolipoyl dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
thiamine biosynthetic process go/ biological_process
cell redox homeostasis go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Citrate cycle (TCA cycle) kegg/ kegg pathway
Glycine serine and threonine metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
lipoamide_DH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0962
(Mouseover regulator name to see its description)

RSP_0962 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_0962 (23)
Regulator Module Operator
RSP_0728 190 tf
RSP_0755 190 tf
RSP_1286 190 tf
RSP_1712 190 tf
RSP_2165 190 tf
RSP_2346 190 tf
RSP_2572 190 tf
RSP_2801 190 tf
RSP_2838 190 tf
RSP_2850 190 tf
RSP_2965 190 tf
RSP_3001 190 tf
RSP_3226 190 tf
RSP_3322 190 tf
RSP_3664 190 tf
RSP_0623 208 tf
RSP_0722 208 tf
RSP_0760 208 tf
RSP_1164 208 tf
RSP_1225 208 tf
RSP_1712 208 tf
RSP_1739 208 tf
RSP_1890 208 tf

Warning: RSP_0962 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
8100 2.60e-60 cactctGc.cAAATATCCTCGGGG
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8101 3.00e-28 CgGGGGGCaGACAGCCCCCcG
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8136 2.70e-04 TTtatcctta.ctAaaaaAA
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8137 1.30e+00 CCC.tt.ctGtTG.tt.gaGg
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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_0962

RSP_0962 is enriched for 16 functions in 3 categories.
Enrichment Table (16)
Function System
Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes cog/ cog
dihydrolipoyl dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
electron transport go/ biological_process
thiamine biosynthetic process go/ biological_process
cell redox homeostasis go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Citrate cycle (TCA cycle) kegg/ kegg pathway
Glycine serine and threonine metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
lipoamide_DH tigr/ tigrfam
Module neighborhood information for RSP_0962

RSP_0962 has total of 56 gene neighbors in modules 190, 208
Gene neighbors (56)
Gene Common Name Description Module membership
RSP_0006 RSP_0006 possible transporter, DMT superfamily (NCBI) 159, 190
RSP_0007 RSP_0007 putative outer membrane protein (NCBI) 190, 248
RSP_0009 RSP_0009 hypothetical protein (NCBI) 98, 208
RSP_0183 dht phenylhydantoinase (RefSeq) 156, 190
RSP_0189 RSP_0189 NADPH-dependent glutamate synthase beta chain and related oxidoreductase (NCBI) 43, 208
RSP_0190 accB Biotin carboxyl carrier protein, AccB (NCBI) 43, 208
RSP_0191 accC Biotin carboxylase (NCBI) 43, 208
RSP_0192 aat possible leucyl/phenylalanyl-tRNA--protein transferase (NCBI) 43, 208
RSP_0627 RSP_0627 Putative amidohydrolase (NCBI) 159, 190
RSP_0628 RSP_0628 hypothetical protein (NCBI) 159, 190
RSP_0629 RSP_0629 hypothetical protein (NCBI) 159, 190
RSP_0630 RSP_0630 hypothetical protein (NCBI) 159, 190
RSP_0631 RSP_0631 hypothetical protein (NCBI) 159, 190
RSP_0632 hisD1 Histidinol dehydrogenase (NCBI) 159, 190
RSP_0776 LolD ABC lipoprotein efflux transporter, ATPase subunit, LolD (NCBI) 159, 190
RSP_0777 LolE ABC lipoprotein efflux transporter, inner membrane subunit, LolE (NCBI) 159, 190
RSP_0962 RSP_0962 Dihydrolipoamide dehydrogenase (NCBI) 190, 208
RSP_0963 RSP_0963 Inner membrane protein (NCBI) 208, 221
RSP_0964 sucB Dihydrolipoamide transsuccinylase (NCBI) 208, 297
RSP_0965 sucA 2-oxoglutarate dehydrogenase E1 component (RefSeq) 208, 297
RSP_0966 sucD Succinyl-CoA synthetase, alpha subunit (NCBI) 208, 297
RSP_0967 sucC Succinyl-CoA synthetase, beta subunit (NCBI) 208, 297
RSP_0970 RSP_0970 Putative citrate lyase beta chain (NCBI) 208, 263
RSP_1046 RSP_1046 hypothetical protein (NCBI) 156, 190
RSP_1060 rnpA Ribonuclease P protein component (NCBI) 182, 208
RSP_1061 RSP_1061 hypothetical protein (NCBI) 65, 208
RSP_1071 moaE Molybdopterin converting factor subunit 2 (NCBI) 154, 208
RSP_1074 uvrC Excinuclease ABC, C subunit (NCBI) 208, 340
RSP_1125 MltB Membrane bound lytic murein transglycosylase B (NCBI) 156, 190
RSP_1552 RSP_1552 putative ureidoglycolate hydrolase (NCBI) 156, 190
RSP_1622 RSP_1622 Putative DNA-binding protein (NCBI) 93, 208
RSP_1624 RSP_1624 hypothetical protein (NCBI) 48, 208
RSP_1697 RSP_1697 hypothetical protein (NCBI) 156, 190
RSP_1841 RSP_1841 Probable intracellular septation protein (NCBI) 156, 190
RSP_1842 RSP_1842 possible transporter, DME family, DMT superfamily (NCBI) 156, 190
RSP_1975 RSP_1975 aminopeptidase P (NCBI) 208, 326
RSP_2137 RSP_2137 hypothetical protein (NCBI) 156, 190
RSP_2138 fumC Fumarate lyase (NCBI) 156, 190
RSP_2143 RSP_2143 DNA photolyase, Cryptochrome 1 apoprotein (Blue light photoreceptor) (NCBI) 159, 190
RSP_2297 atpA F0F1-type ATP synthase alpha subunit (NCBI) 208, 369
RSP_2423 RSP_2423 putative Heat shock protein 15 (HSP15) (NCBI) 65, 208
RSP_2804 tgt Probable queuine tRNA ribosyltransferase (NCBI) 190, 258
RSP_2906 RSP_2906 Putative methylase (NCBI) 159, 190
RSP_2924 RSP_2924 ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) 65, 208
RSP_2925 RSP_2925 ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) 65, 208
RSP_2926 RSP_2926 ABC branched-chain amino acid transporter family, inner membrane subunit (NCBI) 65, 208
RSP_2928 RSP_2928 hypothetical protein (NCBI) 65, 208
RSP_3596 lnt Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (NCBI) 156, 190
RSP_3661 RSP_3661 TRAP-T family transporter, periplasmic binding protein (NCBI) 208, 342
RSP_3662 RSP_3662 TRAP-T family transporter, large (12TMs) inner membrane subunit (NCBI) 208, 342
RSP_6054 RSP_6054 hypothetical protein (NCBI) 190, 194
RSP_6069 RSP_6069 hypothetical protein (NCBI) 190, 194
RSP_6152 RSP_6152 hypothetical protein (NCBI) 33, 190
RSP_6181 RSP_6181 None 190, 248
RSP_6188 RSP_6188 hypothetical protein (NCBI) 190, 194
RSP_6242 RSP_6242 hypothetical protein (NCBI) 190, 194
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_0962
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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