Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0663 cysK

cysteine synthase A

CircVis
Functional Annotations (11)
Function System
Cysteine synthase cog/ cog
cysteine synthase activity go/ molecular_function
cysteine biosynthetic process from serine go/ biological_process
cysteine synthase complex go/ cellular_component
pyridoxal phosphate binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Selenocompound metabolism kegg/ kegg pathway
Sulfur metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
cysKM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0663
(Mouseover regulator name to see its description)

DVU0663 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU0663 cysK (21)
Regulator Module Operator
DVU0813
DVU0230
218 combiner
DVU0854 218 tf
DVU0916 218 tf
DVU1628
DVU0813
218 combiner
DVU1788
DVU1340
218 combiner
DVU2086 218 tf
DVU2547
DVU1788
218 combiner
DVU2547
DVU2086
218 combiner
DVU3186
DVU0269
218 combiner
DVU0744
DVU0525
4 combiner
DVU0813
DVU0230
4 combiner
DVU0854 4 tf
DVU0936 4 tf
DVU1584 4 tf
DVU1628 4 tf
DVU1628
DVU0813
4 combiner
DVU1730 4 tf
DVU1788 4 tf
DVU2086 4 tf
DVU2547 4 tf
DVU3381 4 tf

Warning: DVU0663 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
7 3.10e+00 AaatGcAgaAA
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RegPredict
8 2.60e+03 tGcAaggggGCAa
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RegPredict
415 1.60e+03 caTTaCgaaGcAaaaaaGaaC
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RegPredict
416 1.10e+04 TaATtATATT
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RegPredict
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 DVU0663

DVU0663 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Cysteine synthase cog/ cog
cysteine synthase activity go/ molecular_function
cysteine biosynthetic process from serine go/ biological_process
cysteine synthase complex go/ cellular_component
pyridoxal phosphate binding go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Selenocompound metabolism kegg/ kegg pathway
Sulfur metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
cysKM tigr/ tigrfam
Module neighborhood information for DVU0663

DVU0663 has total of 31 gene neighbors in modules 4, 218
Gene neighbors (31)
Gene Common Name Description Module membership
DVU0483 DNA mismatch repair protein MutL 4, 57
DVU0595 hypothetical protein DVU0595 4, 194
DVU0662 cysE serine O-acetyltransferase 4, 120
DVU0663 cysK cysteine synthase A 4, 218
DVU0664 cysteine desulfurase 4, 120
DVU0665 nitrogen fixation protein nifU 209, 218
DVU0725 hypothetical protein DVU0725 4, 194
DVU0811 dnaK molecular chaperone DnaK 104, 218
DVU0812 grpE heat shock protein GrpE 4, 218
DVU0825 secA preprotein translocase subunit SecA 218, 227
DVU0857 radical SAM domain-containing protein 158, 218
DVU0994 hypothetical protein DVU0994 158, 218
DVU1013 TolC family type I secretion outer membrane protein 4, 110
DVU1212 fsxA fxsA protein 4, 120
DVU1468 peptidase/PDZ domain-containing protein 104, 218
DVU1629 yfiA ribosomal subunit interface protein 4, 90
DVU1839 trx thioredoxin 4, 167
DVU1874 clpB ATP-dependent Clp protease, ATP-binding subunit ClpB 4, 158
DVU1976 groEL chaperonin GroEL 104, 218
DVU1977 groES co-chaperonin GroES 104, 218
DVU2078 cheB-2 protein-glutamate methylesterase CheB 104, 218
DVU2079 sensory box histidine kinase 104, 218
DVU2324 copper-translocating P-type ATPase 4, 194
DVU2439 RND family efflux transporter MFP subunit 4, 110
DVU2467 rnr ribonuclease R 4, 316
DVU2468 lpxK tetraacyldisaccharide 4'-kinase 4, 194
DVU2469 hypothetical protein DVU2469 4, 167
DVU2643 htpG heat shock protein 90 104, 218
DVU2974 hypothetical protein DVU2974 4, 194
DVU3283 hypothetical protein DVU3283 4, 57
DVU3316 pyrD dihydroorotate dehydrogenase 4, 110
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 DVU0663
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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