Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1871 aspA

aspartate ammonia-lyase

CircVis
Functional Annotations (8)
Function System
Aspartate ammonia-lyase cog/ cog
fumarate metabolic process go/ biological_process
aspartate metabolic process go/ biological_process
aspartate ammonia-lyase activity go/ molecular_function
tricarboxylic acid cycle enzyme complex go/ cellular_component
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1871
(Mouseover regulator name to see its description)

DVU1871 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU1871 aspA (20)
Regulator Module Operator
DVU0030
DVU2567
118 combiner
DVU1063 118 tf
DVU1517 118 tf
DVU1518
DVU2195
118 combiner
DVU1561
DVUA0024
118 combiner
DVU1561
DVUA0143
118 combiner
DVU1754 118 tf
DVU2785
DVU3142
118 combiner
DVU2832 118 tf
DVUA0024
DVU0529
118 combiner
DVU0804
DVU3142
79 combiner
DVU1063 79 tf
DVU1517 79 tf
DVU1561
DVU2832
79 combiner
DVU1561
DVUA0024
79 combiner
DVU1754 79 tf
DVU1754
DVU1561
79 combiner
DVU2567 79 tf
DVU3142 79 tf
DVUA0024 79 tf

Warning: DVU1871 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
155 4.30e+01 acCgaGGgg.TtttCttgtAa
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RegPredict
156 6.70e+03 aCatcaAAaCg
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RegPredict
227 1.50e+04 CgTTgC
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RegPredict
228 3.80e+04 ATGAAA
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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 DVU1871

DVU1871 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Aspartate ammonia-lyase cog/ cog
fumarate metabolic process go/ biological_process
aspartate metabolic process go/ biological_process
aspartate ammonia-lyase activity go/ molecular_function
tricarboxylic acid cycle enzyme complex go/ cellular_component
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for DVU1871

DVU1871 has total of 24 gene neighbors in modules 79, 118
Gene neighbors (24)
Gene Common Name Description Module membership
DVU0609 lipoprotein 19, 118
DVU0824 hypothetical protein DVU0824 1, 79
DVU1098 adenine specific DNA methyltransferase 118, 244
DVU1110 hypothetical protein DVU1110 118, 239
DVU1356 HD domain-containing protein 84, 118
DVU1417 hypothetical protein DVU1417 79, 80
DVU1493 hypothetical protein DVU1493 79, 129
DVU1598 hypothetical protein DVU1598 86, 118
DVU1702 hypothetical protein DVU1702 79, 118
DVU1703 type I restriction-modification enzyme, R subunit 118, 270
DVU1753 hypothetical protein DVU1753 118, 242
DVU1755 hypothetical protein DVU1755 118, 133
DVU1761 hypothetical protein DVU1761 79, 295
DVU1870 cyclase 79, 85
DVU1871 aspA aspartate ammonia-lyase 79, 118
DVU2132 hypothetical protein DVU2132 118, 138
DVU2133 hypothetical protein DVU2133 118, 138
DVU2167 hypothetical protein DVU2167 79, 295
DVU2196 hypothetical protein DVU2196 85, 118
DVU2207 hypothetical protein DVU2207 118, 243
DVU2270 hypothetical protein DVU2270 97, 118
DVU2719 hypothetical protein DVU2719 20, 79
DVU2724 phage baseplate assembly protein V 20, 79
DVU2808 TonB domain-containing protein 7, 118
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 DVU1871
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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