Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1128 dapE

succinyl-diaminopimelate desuccinylase (NCBI)

CircVis
Functional Annotations (10)
Function System
Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
succinyl-diaminopimelate desuccinylase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
protein dimerization activity go/ molecular_function
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapE_proteo tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1128
(Mouseover regulator name to see its description)

RSP_1128 is regulated by 20 influences and regulates 0 modules.
Regulators for RSP_1128 dapE (20)
Regulator Module Operator
RSP_0087 316 tf
RSP_0623 316 tf
RSP_1139 316 tf
RSP_1220 316 tf
RSP_1518 316 tf
RSP_2324 316 tf
RSP_2610 316 tf
RSP_3238 316 tf
RSP_3317 316 tf
RSP_0443 69 tf
RSP_1191 69 tf
RSP_1243 69 tf
RSP_1741 69 tf
RSP_2324 69 tf
RSP_2346 69 tf
RSP_2362 69 tf
RSP_2425 69 tf
RSP_2494 69 tf
RSP_2850 69 tf
RSP_3001 69 tf

Warning: RSP_1128 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
7858 1.30e+03 GATCtcG
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7859 1.80e+04 AGCCTGaCTTT
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8344 6.30e-03 AtAATATT
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8345 6.00e-01 aagCCagAACAAgtAgCacAG
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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_1128

RSP_1128 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
succinyl-diaminopimelate desuccinylase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
protein dimerization activity go/ molecular_function
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
dapE_proteo tigr/ tigrfam
Module neighborhood information for RSP_1128

RSP_1128 has total of 26 gene neighbors in modules 69, 316
Gene neighbors (26)
Gene Common Name Description Module membership
RSP_0425 metG Methionyl-tRNA synthetase (NCBI) 311, 316
RSP_0478 RSP_0478 putative lysyl-tRNA synthetase (NCBI) 183, 316
RSP_0567 RSP_0567 Probable Methylated-DNA-(protein)-cysteine S-methyltransferase (NCBI) 316, 337
RSP_0772 parE DNA topoisomerase II/DNA gyrase, subunit B (NCBI) 69, 267
RSP_0819 rhlE2 DEAD/DEAH box helicase (NCBI) 209, 316
RSP_0830 RSP_0830 CBS-domain-containing membrane protein (NCBI) 54, 69
RSP_0903 RSP_0903 Catalase (NCBI) 69, 265
RSP_0933 RSP_0933 hypothetical protein (NCBI) 69, 101
RSP_1011 RSP_1011 hypothetical protein (NCBI) 69, 164
RSP_1128 dapE succinyl-diaminopimelate desuccinylase (NCBI) 69, 316
RSP_1426 RSP_1426 RNA-binding region RNP-1 (NCBI) 209, 316
RSP_1427 RSP_1427 hypothetical protein (NCBI) 209, 316
RSP_1832 RSP_1832 peptidase, M16 family (NCBI) 69, 268
RSP_1988 RSP_1988 hypothetical protein (NCBI) 13, 69
RSP_2254 RSP_2254 ABC efflux transporter, fused ATPase and inner membrane subunits (NCBI) 115, 316
RSP_2409 rluD putative Pseudouridine synthase, Rlu (NCBI) 54, 316
RSP_2552 exoU Glycosyl transferase, family 2 (NCBI) 209, 316
RSP_2558 RSP_2558 hypothetical protein (NCBI) 157, 316
RSP_2659 dgt Deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 117, 316
RSP_3005 RSP_3005 hypothetical protein (NCBI) 40, 316
RSP_3006 RSP_3006 conserved hypothetical protein containing Von Willebrand factor, type A domain (NCBI) 40, 316
RSP_3317 RSP_3317 transcriptional regulator, TetR family (NCBI) 247, 316
RSP_3318 acrB Cation/multidrug efflux pump, RND family (NCBI) 301, 316
RSP_3321 acrA Cation/multidrug efflux pump, membrane-fusion protein (NCBI) 301, 316
RSP_3435 RSP_3435 possible DNA-binding protein (NCBI) 91, 316
RSP_3658 hpcH putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (NCBI) 105, 316
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_1128
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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