Organism : Bacillus subtilis | Module List :
BSU04000 ycsA

tartrate dehydrogenase (RefSeq)

CircVis
Functional Annotations (7)
Function System
Isocitrate/isopropylmalate dehydrogenase cog/ cog
metabolic process go/ biological_process
tartrate dehydrogenase activity go/ molecular_function
NAD binding go/ molecular_function
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
TTC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU04000
(Mouseover regulator name to see its description)

BSU04000 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU04000 ycsA (22)
Regulator Module Operator
BSU02890 411 tf
BSU14740 411 tf
BSU18760 411 tf
BSU20010 411 tf
BSU25760 411 tf
BSU26580 411 tf
BSU26870 411 tf
BSU27080 411 tf
BSU28410 411 tf
BSU00980 168 tf
BSU02000 168 tf
BSU02550 168 tf
BSU03750 168 tf
BSU03890 168 tf
BSU04250 168 tf
BSU06960 168 tf
BSU07590 168 tf
BSU08100 168 tf
BSU08370 168 tf
BSU22120 168 tf
BSU23100 168 tf
BSU26870 168 tf

Warning: BSU04000 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
5284 2.60e+00 atcctcA.atAaaaGgAgGT
Loader icon
5285 1.60e+02 aTtAataaAagcccTtcCaa
Loader icon
5726 1.30e-04 cCTcCTTTttc
Loader icon
5727 6.30e+04 GACAaGGGg
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 BSU04000

BSU04000 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Isocitrate/isopropylmalate dehydrogenase cog/ cog
metabolic process go/ biological_process
tartrate dehydrogenase activity go/ molecular_function
NAD binding go/ molecular_function
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
TTC tigr/ tigrfam
Module neighborhood information for BSU04000

BSU04000 has total of 47 gene neighbors in modules 168, 411
Gene neighbors (47)
Gene Common Name Description Module membership
BSU02130 glpQ glycerophosphoryl diester phosphodiesterase (RefSeq) 285, 411
BSU02140 glpT glycerol-3-phosphate permease (RefSeq) 285, 411
BSU02460 ycbC 5-dehydro-4-deoxyglucarate dehydratase (RefSeq) 168, 326
BSU02470 ycbD 2,5-dioxovalerate dehydrogenase (alpha-ketoglutaric semialdehyde dehydrogenase) (RefSeq) 168, 326
BSU02490 gudD glucarate dehydratase (RefSeq) 86, 168
BSU02530 rtpA anti-TRAP regulator (RefSeq) 102, 168
BSU02550 ycbL two-component response regulator [YcbM] (RefSeq) 168, 219
BSU03530 ycxA putative permease (RefSeq) 71, 168
BSU04000 ycsA tartrate dehydrogenase (RefSeq) 168, 411
BSU04470 dctP C4-dicarboxylate transporter DctA (RefSeq) 55, 168
BSU05190 ydeG putative permease (RefSeq) 168, 290
BSU05740 phoB alkaline phosphatase III (RefSeq) 86, 411
BSU08010 yfjP putative DNA-modified purine glycosidase (RefSeq) 114, 168
BSU08170 yfjA hypothetical protein (RefSeq) 92, 168
BSU09300 glpD glycerol-3-phosphate oxidase (RefSeq) 22, 411
BSU09440 citA citrate synthase I (RefSeq) 102, 411
BSU10170 fabHB 3-oxoacyl-(acyl carrier protein) synthase III (RefSeq) 307, 411
BSU10500 yhjG hypothetical protein (RefSeq) 168, 285
BSU11320 yjzB hypothetical protein (RefSeq) 307, 411
BSU11410 yjbA putative nucleic acid binding protein (RefSeq) 127, 411
BSU12010 manP phosphotransferase system (PTS) mannose-specific enzyme IIBCA component (RefSeq) 61, 168
BSU17520 ynaD putative N-acetyltransferase (RefSeq) 219, 411
BSU17580 xynB xylan beta-1,4-xylosidase (RefSeq) 168, 321
BSU18170 yngA putative conserved membrane protein (RefSeq) 168, 189
BSU18700 yoaQ hypothetical protein (RefSeq) 129, 411
BSU18860 yozH hypothetical protein (RefSeq) 246, 411
BSU19250 yocL hypothetical protein (RefSeq) 202, 411
BSU19260 yocM putative spore coat protein (RefSeq) 16, 411
BSU19520 yojA putative H+/anion permease (RefSeq) 61, 168
BSU19600 yodH putative S-adenosylmethionine-dependent methyltransferase (RefSeq) 280, 411
BSU22090 kdgT 2-keto-3-deoxygluconate permease (RefSeq) 152, 168
BSU22100 kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase (RefSeq) 152, 168
BSU22110 kdgK 2-keto-3-deoxygluconate kinase (RefSeq) 152, 168
BSU22120 kdgR Kdg operon transcriptional regulator (LacI family) (RefSeq) 168, 223
BSU22130 kduI 5-keto-4-deoxyuronate isomerase (RefSeq) 142, 168
BSU22140 kduD 2-deoxy-D-gluconate 3-dehydrogenase (RefSeq) 150, 168
BSU24580 yqhH putative RNA polymerase-associated helicase protein (RefSeq) 55, 411
BSU24590 yqhG hypothetical protein (RefSeq) 239, 411
BSU26860 yraO putative citrate transporter (RefSeq) 152, 168
BSU26870 yraN putative transcriptional regulator (LysR family) (RefSeq) 152, 168
BSU27310 pbpI penicillin-binding protein PBP4B (RefSeq) 304, 411
BSU31470 kapD sporulation inhibitor KapD (RefSeq) 238, 411
BSU32340 lytH sporulation-specific L-Ala-D-Glu endopeptidase (RefSeq) 43, 411
BSU32950 yusW putative lipoprotein (RefSeq) 55, 411
BSU35280 yvjA putative integral inner membrane protein (RefSeq) 307, 411
BSU38230 ywcB putative phage protein (superinfection immunity) (RefSeq) 33, 411
BSU39420 deoC deoxyribose-phosphate aldolase (RefSeq) 168, 285
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 BSU04000
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