Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2330 leuA

2-Isopropylmalate synthase (NCBI)

CircVis
Functional Annotations (10)
Function System
Isopropylmalate/homocitrate/citramalate synthases cog/ cog
2-isopropylmalate synthase activity go/ molecular_function
cysteine-type endopeptidase activity go/ molecular_function
proteolysis go/ biological_process
leucine biosynthetic process go/ biological_process
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
leuA_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2330
(Mouseover regulator name to see its description)

RSP_2330 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_2330 leuA (28)
Regulator Module Operator
RSP_0601 286 tf
RSP_0607 286 tf
RSP_0958 286 tf
RSP_1034 286 tf
RSP_1274 286 tf
RSP_1892 286 tf
RSP_1922 286 tf
RSP_2130 286 tf
RSP_2201 286 tf
RSP_2610 286 tf
RSP_3324 286 tf
RSP_3464 286 tf
RSP_3680 286 tf
RSP_3748 286 tf
RSP_0728 185 tf
RSP_0794 185 tf
RSP_0999 185 tf
RSP_1139 185 tf
RSP_1871 185 tf
RSP_1945 185 tf
RSP_2324 185 tf
RSP_2410 185 tf
RSP_2719 185 tf
RSP_2801 185 tf
RSP_2850 185 tf
RSP_2889 185 tf
RSP_3238 185 tf
RSP_3665 185 tf

Warning: RSP_2330 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
8090 2.70e-01 TCccagaAatggAaG
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8091 2.00e-01 CCtT.TtcTgCgGgg.AtgGA
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8286 1.30e+00 cgaaggTcaGgcAaagGatcg
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8287 4.00e+02 GtCgTTTcaaaCattTcGcGG
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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_2330

RSP_2330 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Isopropylmalate/homocitrate/citramalate synthases cog/ cog
2-isopropylmalate synthase activity go/ molecular_function
cysteine-type endopeptidase activity go/ molecular_function
proteolysis go/ biological_process
leucine biosynthetic process go/ biological_process
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
leuA_bact tigr/ tigrfam
Module neighborhood information for RSP_2330

RSP_2330 has total of 46 gene neighbors in modules 185, 286
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0339 RSP_0339 hypothetical protein (NCBI) 280, 286
RSP_0365 RSP_0365 hypothetical protein (NCBI) 107, 185
RSP_0460 RSP_0460 AcrB/AcrD/AcrF family cation/multidrug efflux pump (NCBI) 111, 185
RSP_0461 RSP_0461 multidrug/cation efflux pump, membrane fusion protein (MFP) family (NCBI) 111, 185
RSP_0548 RSP_0548 hypothetical protein (NCBI) 185, 250
RSP_0589 RSP_0589 hypothetical protein (NCBI) 185, 250
RSP_0671 RSP_0671 ExbD/TolR family protein (NCBI) 286, 294
RSP_0672 TolQ Biopolymer transport protein, TolQ (NCBI) 277, 286
RSP_0795 RSP_0795 hypothetical protein (NCBI) 107, 185
RSP_0799 RSP_0799 hypothetical protein (NCBI) 286, 287
RSP_0923 map1 Methionine aminopeptidase, subfamily 1 (NCBI) 84, 286
RSP_0924 cinA Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI) 71, 286
RSP_0925 yobR Putative acetyl transferase (NCBI) 84, 286
RSP_0926 RSP_0926 OmpA/MotB family protein (NCBI) 84, 286
RSP_0958 RSP_0958 RAM domain protein (NCBI) 82, 286
RSP_1023 RSP_1023 hypothetical protein (NCBI) 185, 200
RSP_1260 RSP_1260 hypothetical protein (NCBI) 207, 286
RSP_1421 RSP_1421 hypothetical protein (NCBI) 286, 366
RSP_1542 RSP_1542 ABC transporter, ATPase subunit (NCBI) 210, 286
RSP_1672 pdxJ PNP synthase, pyridoxal phosphate biosynthetic protein PdxJ (NCBI) 181, 286
RSP_1834 RSP_1834 hypothetical protein (NCBI) 10, 185
RSP_1880 RSP_1880 hypothetical protein (NCBI) 64, 185
RSP_1939 RSP_1939 NADPH-ferredoxin reductase (NCBI) 86, 185
RSP_1945 RSP_1945 Transcriptional Regulator, AsnC family (NCBI) 86, 185
RSP_1956 RSP_1956 hypothetical protein (NCBI) 280, 286
RSP_2122 mtbC Putative dimethylamine corrinoid protein (NCBI) 185, 285
RSP_2201 RSP_2201 transcriptional regulator, MerR family (NCBI) 162, 286
RSP_2330 leuA 2-Isopropylmalate synthase (NCBI) 185, 286
RSP_2374 RSP_2374 hypothetical protein (NCBI) 218, 286
RSP_2387 RSP_2387 hypothetical protein (NCBI) 71, 286
RSP_2646 RSP_2646 None 286, 309
RSP_2671 RSP_2671 hypothetical protein (NCBI) 35, 185
RSP_2847 RSP_2847 hypothetical protein (NCBI) 185, 250
RSP_2889 RSP_2889 Transcriptional regulator (NCBI) 185, 229
RSP_2890 RSP_2890 Copper-translocating P-type ATPase (NCBI) 185, 229
RSP_2891 RSP_2891 Putative copper chaperone (NCBI) 185, 229
RSP_2892 RSP_2892 hypothetical protein (NCBI) 185, 308
RSP_2973 RSP_2973 Peroxiredoxin (NCBI) 158, 286
RSP_2982 gcpE Probable 4-hydroxy-3-methylbut-2-en-1-yl diphosphate (NCBI) 64, 185
RSP_3082 RSP_3082 hypothetical protein (NCBI) 185, 213
RSP_3228 RSP_3228 Predicted mannose-6-phosphate isomerase (NCBI) 35, 185
RSP_3263 RSP_3263 Putative copper binding protein (NCBI) 27, 185
RSP_3307 RSP_3307 hypothetical protein (NCBI) 35, 185
RSP_3324 RSP_3324 transcriptional regulator, LuxR family (NCBI) 46, 286
RSP_3594 RSP_3594 Antifreeze protein, type I (NCBI) 35, 185
RSP_4312 RSP_4312 tRNA-Glu (NCBI) 185, 225
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_2330
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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