Organism : Bacillus subtilis | Module List :
BSU09440 citA

citrate synthase I (RefSeq)

CircVis
Functional Annotations (7)
Function System
Citrate synthase cog/ cog
citrate (Si)-synthase activity go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU09440
(Mouseover regulator name to see its description)

BSU09440 is regulated by 23 influences and regulates 0 modules.
Regulators for BSU09440 citA (23)
Regulator Module Operator
BSU03080 102 tf
BSU08990 102 tf
BSU09060 102 tf
BSU09330 102 tf
BSU11500 102 tf
BSU18460 102 tf
BSU29740 102 tf
BSU30020 102 tf
BSU30260 102 tf
BSU33080 102 tf
BSU33840 102 tf
BSU36630 102 tf
BSU38220 102 tf
BSU40710 102 tf
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

Warning: BSU09440 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
5158 8.40e+00 C.aCCTTTttc
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5159 2.40e+03 gGAaAggAg
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5726 1.30e-04 cCTcCTTTttc
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5727 6.30e+04 GACAaGGGg
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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 BSU09440

BSU09440 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Citrate synthase cog/ cog
citrate (Si)-synthase activity go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Glyoxylate and dicarboxylate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for BSU09440

BSU09440 has total of 44 gene neighbors in modules 102, 411
Gene neighbors (44)
Gene Common Name Description Module membership
BSU02130 glpQ glycerophosphoryl diester phosphodiesterase (RefSeq) 285, 411
BSU02140 glpT glycerol-3-phosphate permease (RefSeq) 285, 411
BSU02530 rtpA anti-TRAP regulator (RefSeq) 102, 168
BSU04000 ycsA tartrate dehydrogenase (RefSeq) 168, 411
BSU05250 ydeM putative dehydratase (RefSeq) 23, 102
BSU05740 phoB alkaline phosphatase III (RefSeq) 86, 411
BSU08040 yfjM hypothetical protein (RefSeq) 102, 361
BSU08050 yfjL hypothetical protein (RefSeq) 102, 255
BSU09060 yhcF putative transcriptional regulator (GntR family) (RefSeq) 11, 102
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
BSU11320 yjzB hypothetical protein (RefSeq) 307, 411
BSU11410 yjbA putative nucleic acid binding protein (RefSeq) 127, 411
BSU17520 ynaD putative N-acetyltransferase (RefSeq) 219, 411
BSU18700 yoaQ hypothetical protein (RefSeq) 129, 411
BSU18860 yozH hypothetical protein (RefSeq) 246, 411
BSU19220 yocI putative ATP-dependent nucleic acid helicase (RefSeq) 102, 334
BSU19250 yocL hypothetical protein (RefSeq) 202, 411
BSU19260 yocM putative spore coat protein (RefSeq) 16, 411
BSU19480 yojE putative integral inner membrane protein (RefSeq) 102, 255
BSU19590 ctpA carboxy-terminal processing protease (RefSeq) 102, 309
BSU19600 yodH putative S-adenosylmethionine-dependent methyltransferase (RefSeq) 280, 411
BSU20040 nrdF ribonucleotide-diphosphate reductase subunit beta (NCBI) 66, 102
BSU21770 ilvA threonine dehydratase (RefSeq) 102, 155
BSU22030 ypbR putative GTP-binding protein (RefSeq) 102, 179
BSU22720 cheR methyl-accepting chemotaxis proteins (MCPs) methyltransferase (RefSeq) 102, 334
BSU23750 yqjT putative lyase (RefSeq) 102, 334
BSU23840 yqjK ribonuclease Z (RefSeq) 102, 233
BSU24580 yqhH putative RNA polymerase-associated helicase protein (RefSeq) 55, 411
BSU24590 yqhG hypothetical protein (RefSeq) 239, 411
BSU27200 yrhG putative formate/nitrite transporter (RefSeq) 80, 102
BSU27310 pbpI penicillin-binding protein PBP4B (RefSeq) 304, 411
BSU31470 kapD sporulation inhibitor KapD (RefSeq) 238, 411
BSU31490 pbpD penicillin-binding protein 4 (RefSeq) 102, 402
BSU32340 lytH sporulation-specific L-Ala-D-Glu endopeptidase (RefSeq) 43, 411
BSU32630 yurR putative oxidoreductase (RefSeq) 102, 327
BSU32950 yusW putative lipoprotein (RefSeq) 55, 411
BSU34820 bmrA efflux transporter (ATP-binding and permease protein) (RefSeq) 102, 339
BSU35280 yvjA putative integral inner membrane protein (RefSeq) 307, 411
BSU35660 mnaA UDP-N-acetylmannosamine 2-epimerase (RefSeq) 102, 402
BSU37330 argS arginyl-tRNA synthetase (RefSeq) 102, 155
BSU38220 ywcC putative transcriptional regulator (RefSeq) 102, 116
BSU38230 ywcB putative phage protein (superinfection immunity) (RefSeq) 33, 411
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 BSU09440
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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