Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2557 birA

birA bifunctional protein

CircVis
Functional Annotations (9)
Function System
Biotin-(acetyl-CoA carboxylase) ligase cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
biotin-[acetyl-CoA-carboxylase] ligase activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
protein modification process go/ biological_process
Biotin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
birA_ligase tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2557
(Mouseover regulator name to see its description)

DVU2557 is regulated by 24 influences and regulates 41 modules.
Regulators for DVU2557 birA (24)
Regulator Module Operator
DVU0309
DVU1788
148 combiner
DVU0309
DVU2989
148 combiner
DVU0629 148 tf
DVU0916 148 tf
DVU1561
DVU2114
148 combiner
DVU1788 148 tf
DVU2394
DVU0629
148 combiner
DVU2394
DVU1144
148 combiner
DVU2675 148 tf
DVU2675
DVU2394
148 combiner
DVU2989 148 tf
DVU3255
DVU2675
148 combiner
DVUA0151 148 tf
DVU0230
DVU1949
348 combiner
DVU0277
DVU0118
348 combiner
DVU0277
DVU2894
348 combiner
DVU0653
DVU2251
348 combiner
DVU0946
DVU2251
348 combiner
DVU1788 348 tf
DVU2547
DVU0110
348 combiner
DVU2547
DVU2251
348 combiner
DVU2547
DVU3193
348 combiner
DVU2909 348 tf
DVU3220
DVU2251
348 combiner

Warning: DVU2557 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
281 2.90e-02 ggtATGgTGccgca
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RegPredict
282 2.70e+00 CTCCtTGC
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RegPredict
661 6.00e+02 CtTTccaGCcgtcCcGACgtCgGa
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RegPredict
662 1.60e+03 ctgaC.tcCaTaacggtctggtac
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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 DVU2557

DVU2557 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Biotin-(acetyl-CoA carboxylase) ligase cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
biotin-[acetyl-CoA-carboxylase] ligase activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
protein modification process go/ biological_process
Biotin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
birA_ligase tigr/ tigrfam
Module neighborhood information for DVU2557

DVU2557 has total of 59 gene neighbors in modules 148, 348
Gene neighbors (59)
Gene Common Name Description Module membership
DVU0006 universal stress protein 132, 148
DVU0019 ngr nigerythrin 60, 348
DVU0092 sensory box histidine kinase 145, 348
DVU0138 response regulator 132, 148
DVU0174 hypothetical protein DVU0174 148, 241
DVU0175 tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein 192, 348
DVU0220 tail fiber protein 148, 314
DVU0238 hypothetical protein DVU0238 132, 148
DVU0253 oxidoreductase 148, 153
DVU0260 response regulator 346, 348
DVU0263 acidic cytochrome c3 346, 348
DVU0264 ferredoxin, 4Fe-4S 346, 348
DVU0278 glyoxalase family protein 148, 285
DVU0305 ferredoxin II 132, 148
DVU0402 dsvA dissimilatory sulfite reductase subunit alpha 292, 348
DVU0403 dvsB dissimilatory sulfite reductase subunit beta 292, 348
DVU0404 dissimilatory sulfite reductase B 292, 348
DVU0701 glcB malate synthase G 192, 348
DVU0883 glutaredoxin 60, 148
DVU0979 dihydroxyacetone kinase subunit DhaK 60, 348
DVU0980 DAK2 domain-containing protein 6, 348
DVU1179 aor tungsten-containing aldehyde:ferredoxin oxidoreductase 157, 348
DVU1568 ferritin 132, 148
DVU1569 porA pyruvate ferredoxin oxidoreductase subunit alpha 148, 153
DVU1681 mreB-2 rod shape-determining protein MreB 318, 348
DVU1684 gcvT glycine cleavage system T protein 318, 348
DVU1685 16S ribosomal RNA methyltransferase RsmE 318, 348
DVU1686 recombination factor protein RarA 318, 348
DVU1812 cytochrome c oxidase subunit II 11, 148
DVU1816 hypothetical protein DVU1816 148, 153
DVU1904 cheW-2 chemotaxis protein CheW 132, 148
DVU1917 hysB periplasmic 139, 348
DVU1918 hysA periplasmic 139, 348
DVU1921 hynB-1 periplasmic 229, 348
DVU1922 hynA-1 periplasmic 229, 348
DVU2076 cheR-2 chemotaxis protein methyltransferase 132, 148
DVU2109 hypothetical protein DVU2109 236, 348
DVU2202 transglycosylase 132, 148
DVU2481 formate dehydrogenase subunit beta 77, 348
DVU2482 fdnG-2 formate dehydrogenase subunit alpha, selenocysteine-containing 192, 348
DVU2483 cytochrome c family protein 77, 348
DVU2514 pyk pyruvate kinase 249, 348
DVU2557 birA birA bifunctional protein 148, 348
DVU2583 lipoprotein 14, 148
DVU2616 sensory box histidine kinase/response regulator 11, 148
DVU2684 hypothetical protein DVU2684 71, 148
DVU2935 gpmA phosphoglyceromutase 71, 148
DVU2968 sensor histidine kinase/response regulator 148, 192
DVU3037 rhodanese-like domain-containing protein 192, 348
DVU3183 rbO desulfoferrodoxin 60, 348
DVU3184 rubredoxin 60, 348
DVU3185 roO rubredoxin-oxygen oxidoreductase 60, 348
DVU3227 flagellar basal body-associated protein 71, 148
DVU3262 fdrA fumarate reductase flavoprotein subunit 153, 348
DVU3263 frdB fumarate reductase iron-sulfur subunit 148, 348
DVU3293 acetolactate synthase 60, 348
DVU3294 aldehyde dehydrogenase family protein 153, 348
DVU3296 hypothetical protein DVU3296 14, 148
DVU3319 putA proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase 153, 348
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 DVU2557
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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