Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3171

cytochrome c3

CircVis
Functional Annotations (4)
Function System
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3171
(Mouseover regulator name to see its description)

DVU3171 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU3171 (22)
Regulator Module Operator
DVU0057 146 tf
DVU0230 146 tf
DVU0525 146 tf
DVU0606
DVU1690
146 combiner
DVU1730 146 tf
DVU1745 146 tf
DVU2423
DVU0619
146 combiner
DVU2423
DVU1402
146 combiner
DVU2557
DVU1690
146 combiner
DVU2686 146 tf
DVU3193
DVU1690
146 combiner
DVU0277
DVU1690
262 combiner
DVU0277
DVU1745
262 combiner
DVU0525 262 tf
DVU0606
DVU2251
262 combiner
DVU0679
DVU2251
262 combiner
DVU2319
DVU2690
262 combiner
DVU2557
DVU0653
262 combiner
DVU2557
DVU0936
262 combiner
DVU3167
DVU2251
262 combiner
DVU3313 262 tf
DVU3313
DVU0230
262 combiner

Warning: DVU3171 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
279 5.10e-02 GcCaGcttcTACcGGa
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RegPredict
280 8.10e+04 C.ataCgc.T.tacTc.GtgAcgg
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RegPredict
499 1.00e+02 TtGtgAAA
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RegPredict
500 9.80e+03 Aaa.tgtGCttTccCgcTcCaTt
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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 DVU3171

DVU3171 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
Module neighborhood information for DVU3171

DVU3171 has total of 54 gene neighbors in modules 146, 262
Gene neighbors (54)
Gene Common Name Description Module membership
DVU0041 Slt family transglycosylase 145, 146
DVU0095 polyamine ABC transporter periplasmic polyamine-binding protein 139, 262
DVU0096 potC spermidine/putrescine ABC transporter membrane protein 139, 262
DVU0386 amino acid ABC transporter periplasmic amino acid-binding protein 262, 288
DVU0477 icd isocitrate dehydrogenase, NADP-dependent 230, 262
DVU0712 amino acid ABC transporter periplasmic-binding protein 262, 331
DVU0841 aspartate aminotransferase 146, 344
DVU0896 NLP/P60 family lipoprotein 78, 146
DVU0899 hypothetical protein DVU0899 146, 172
DVU0936 hypothetical protein DVU0936 146, 232
DVU0937 hypothetical protein DVU0937 11, 262
DVU0965 hypothetical protein DVU0965 146, 215
DVU0966 amino acid ABC transporter periplasmic amino acid-binding protein 146, 306
DVU1038 hisA 1-(5-phosphoribosyl)-5- 146, 288
DVU1064 aconitate hydratase 14, 146
DVU1067 Bmp family membrane protein 146, 221
DVU1095 argG argininosuccinate synthase 220, 262
DVU1238 amino acid ABC transporter periplasmic amino acid-binding protein 146, 255
DVU1392 NLP/P60 family protein 146, 232
DVU1406 purM phosphoribosylaminoimidazole synthetase 88, 146
DVU1423 lpdA 2-oxoglutarate dehydrogenase, E3 component, lipoamide dehydrogenase 14, 146
DVU1615 paaK-2 phenylacetate-coenzyme A ligase 146, 323
DVU1777 cynT carbonic anhydrase 179, 262
DVU1910 YjeF-like protein 146, 249
DVU1912 hypothetical protein DVU1912 81, 262
DVU1934 phosphonate ABC transporter permease 33, 262
DVU1937 phosphonate ABC transporter periplasmic phosphonate-binding protein 145, 262
DVU1954 nadD nicotinate (nicotinamide) nucleotide adenylyltransferase 56, 146
DVU1990 hypothetical protein DVU1990 146, 196
DVU2056 hypothetical protein DVU2056 54, 146
DVU2098 cooS carbon monoxide dehydrogenase 179, 262
DVU2150 dnaK suppressor protein 146, 297
DVU2205 tryptophan-specific transport protein 255, 262
DVU2251 DNA-binding protein 135, 146
DVU2342 amino acid ABC transporter periplasmic amino acid-binding protein 178, 262
DVU2347 argD acetylornithine aminotransferase 139, 262
DVU2348 dut deoxyuridine 5'-triphosphate nucleotidohydrolase 153, 262
DVU2364 class I/II aminotransferase 146, 262
DVU2529 pgk phosphoglycerate kinase 262, 296
DVU2782 hypothetical protein DVU2782 26, 146
DVU2783 hypothetical protein DVU2783 146, 195
DVU2791 cytochrome c family protein 139, 146
DVU2792 electron transport complex protein RnfC 139, 262
DVU2793 electron transport complex protein RnfD 139, 262
DVU2794 electron transport complex protein RnfG 139, 262
DVU2795 electron transport complex RsxE subunit 139, 262
DVU2796 electron transport complex protein RnfA 139, 262
DVU2798 ApbE family protein 139, 262
DVU2931 sensory box histidine kinase 75, 262
DVU2940 hypothetical protein DVU2940 146, 215
DVU3171 cytochrome c3 146, 262
DVU3187 hup-4 DNA-binding protein HU 146, 232
DVU3238 response regulator 146, 157
DVU3277 hypothetical protein DVU3277 146, 337
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 DVU3171
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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