Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0571 ald

alanine dehydrogenase

CircVis
Functional Annotations (8)
Function System
Alanine dehydrogenase cog/ cog
alanine dehydrogenase activity go/ molecular_function
electron transport go/ biological_process
alanine metabolic process go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Taurine and hypotaurine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
alaDH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0571
(Mouseover regulator name to see its description)

DVU0571 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU0571 ald (25)
Regulator Module Operator
DVU0682 175 tf
DVU0682
DVU1788
175 combiner
DVU0682
DVU2953
175 combiner
DVU0936
DVU0118
175 combiner
DVU1419 175 tf
DVU2111
DVU0946
175 combiner
DVU2111
DVU1949
175 combiner
DVU2557 175 tf
DVU2588
DVU0118
175 combiner
DVU2956
DVU2319
175 combiner
DVU0569 150 tf
DVU0619
DVU0569
150 combiner
DVU0653
DVU0744
150 combiner
DVU0653
DVU1156
150 combiner
DVU0653
DVU2934
150 combiner
DVU0653
DVUA0100
150 combiner
DVU0744
DVU0569
150 combiner
DVU1063 150 tf
DVU1572
DVU0230
150 combiner
DVU1674 150 tf
DVU1674
DVU0525
150 combiner
DVU1964
DVU1063
150 combiner
DVU3023
DVU0569
150 combiner
DVU3167
DVUA0100
150 combiner
DVUA0151 150 tf

Warning: DVU0571 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
285 3.90e+00 ccATCatC
Loader icon
RegPredict
286 1.30e+02 GctGCGCAgtCaGgCgGC
Loader icon
RegPredict
335 1.30e+02 tttacTCCtTG
Loader icon
RegPredict
336 7.80e+04 aA...GtCatgaaAcaCtttt.Ca
Loader icon
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 DVU0571

DVU0571 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Alanine dehydrogenase cog/ cog
alanine dehydrogenase activity go/ molecular_function
electron transport go/ biological_process
alanine metabolic process go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Taurine and hypotaurine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
alaDH tigr/ tigrfam
Module neighborhood information for DVU0571

DVU0571 has total of 60 gene neighbors in modules 150, 175
Gene neighbors (60)
Gene Common Name Description Module membership
DVU0137 hypothetical protein DVU0137 109, 175
DVU0478 serine/threonine protein phosphatase family protein 14, 150
DVU0489 paaK-1 phenylacetate-coenzyme A ligase 150, 176
DVU0493 hypothetical protein DVU0493 139, 175
DVU0571 ald alanine dehydrogenase 150, 175
DVU0615 hypothetical protein DVU0615 150, 198
DVU0632 cupin family protein 150, 176
DVU0748 acs acetyl-CoA synthetase 150, 296
DVU0767 class V aminotransferase 150, 337
DVU0768 murI glutamate racemase 150, 278
DVU0769 pyridoxamine kinase 150, 278
DVU0902 hypothetical protein 175, 331
DVU1032 hypothetical protein DVU1032 175, 208
DVU1159 hypothetical protein DVU1159 161, 175
DVU1218 hypothetical protein DVU1218 175, 271
DVU1222 hypothetical protein DVU1222 175, 224
DVU1241 hypothetical protein DVU1241 122, 175
DVU1252 hypothetical protein DVU1252 150, 250
DVU1475 PhoU family protein 155, 175
DVU1534 hypothetical protein DVU1534 31, 175
DVU1771 hydC [Fe] hydrogenase gamma [Desulfovibrio vulgaris str. Hildenborough] 175, 198
DVU1797 ksgA dimethyladenosine transferase 75, 150
DVU1817 cyf cytochrome c-553 132, 175
DVU1853 hypothetical protein DVU1853 105, 175
DVU1908 pdxJ pyridoxine 5'-phosphate synthase 33, 150
DVU1944 pyruvate ferredoxin oxidoreductase, iron-sulfur binding subunit 150, 337
DVU1991 hypothetical protein DVU1991 175, 321
DVU1999 sulfate transporter family protein 175, 291
DVU2005 hypothetical protein DVU2005 175, 201
DVU2019 hypothetical protein DVU2019 175, 198
DVU2020 hypothetical protein DVU2020 77, 175
DVU2431 hypothetical protein DVU2431 175, 296
DVU2620 hypothetical protein DVU2620 150, 291
DVU2670 hypothetical protein DVU2670 27, 175
DVU2763 TPR/GGDEF domain-containing protein 175, 198
DVU2776 dsvC dissimilatory sulfite reductase subunit gamma 175, 307
DVU2813 hypothetical protein DVU2813 175, 198
DVU2898 hypothetical protein DVU2898 81, 150
DVU2973 integration host factor subunit beta 132, 175
DVU2995 glycosyl transferase group 1 family protein 150, 278
DVU2996 NAD-dependent epimerase/dehydratase family protein 87, 150
DVU2997 hypothetical protein DVU2997 87, 150
DVU2998 hypothetical protein DVU2998 87, 150
DVU3047 class IV aminotransferase 35, 175
DVU3104 peptidoglycan-associated lipoprotein 6, 175
DVU3126 None 87, 150
DVU3213 hypothetical protein DVU3213 175, 201
DVU3268 hypothetical protein DVU3268 105, 175
DVU3287 glycosyl transferase group 2 family protein 46, 150
DVUA0026 hypothetical protein DVUA0026 175, 233
DVUA0027 hypothetical protein DVUA0027 131, 175
DVUA0028 hypothetical protein DVUA0028 175, 263
DVUA0061 hypothetical protein DVUA0061 53, 150
DVUA0098 dehydrogenase 150, 266
DVUA0112 type III secretion system protein YscC family 136, 150
DVUA0119 type III secretion system ATPase 136, 150
DVUA0124 sigma factor serine-protein kinase 136, 150
DVUA0132 CRISPR-associated Csh2 family protein 131, 150
DVUA0134 cas1 CRISPR-associated Cas1 family protein 150, 266
DVUA0135 CRISPR-associated Cas2 family protein 121, 150
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 DVU0571
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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