Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0633

penicillin-binding protein

CircVis
Functional Annotations (11)
Function System
Membrane carboxypeptidase/penicillin-binding protein cog/ cog
nucleic acid binding go/ molecular_function
peptidase activity go/ molecular_function
penicillin binding go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
transferase activity, transferring pentosyl groups go/ molecular_function
response to antibiotic go/ biological_process
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
PBP_1a_fam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0633
(Mouseover regulator name to see its description)

DVU0633 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU0633 (21)
Regulator Module Operator
DVU0230
DVU1745
141 combiner
DVU0594 141 tf
DVU0653 141 tf
DVU0946 141 tf
DVU1517 141 tf
DVU1518
DVU1561
141 combiner
DVU2785
DVU0529
141 combiner
DVU2785
DVU1517
141 combiner
DVU2788
DVU0653
141 combiner
DVU3023
DVU2319
141 combiner
DVU0230 176 tf
DVU0619
DVU0653
176 combiner
DVU0653 176 tf
DVU0653
DVU2275
176 combiner
DVU1561
DVU1964
176 combiner
DVU1754
DVU1561
176 combiner
DVU2567
DVU2675
176 combiner
DVU2675 176 tf
DVU3167 176 tf
DVU3167
DVU0569
176 combiner
DVUA0024 176 tf

Warning: DVU0633 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
271 4.80e-03 AatTAAAcAAAaGccGaGaaACaC
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RegPredict
272 4.50e+00 GTatCgTgtgGgCtTgcgCcc
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RegPredict
337 2.00e-01 agtt.gCGgCGGGcgaCgacCcg
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RegPredict
338 4.10e+00 cC.CGgAacgcGcctTCggCgCG
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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 DVU0633

DVU0633 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Membrane carboxypeptidase/penicillin-binding protein cog/ cog
nucleic acid binding go/ molecular_function
peptidase activity go/ molecular_function
penicillin binding go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
peptidoglycan-based cell wall go/ cellular_component
transferase activity, transferring pentosyl groups go/ molecular_function
response to antibiotic go/ biological_process
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
PBP_1a_fam tigr/ tigrfam
Module neighborhood information for DVU0633

DVU0633 has total of 57 gene neighbors in modules 141, 176
Gene neighbors (57)
Gene Common Name Description Module membership
DVU0110 sigma-54 dependent transcriptional regulator/response regulator 117, 141
DVU0156 ATP-dependent DNA helicase UvrD 117, 141
DVU0237 serS seryl-tRNA synthetase 29, 176
DVU0296 M24 family peptidase 81, 176
DVU0352 aminotransferase 141, 277
DVU0414 NADP-dependent malic enzyme-like protein 176, 223
DVU0481 rfaD ADP-L-glycero-D-mannoheptose-6-epimerase 166, 176
DVU0487 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit 23, 176
DVU0489 paaK-1 phenylacetate-coenzyme A ligase 150, 176
DVU0632 cupin family protein 150, 176
DVU0633 penicillin-binding protein 141, 176
DVU0635 dolichyl-phosphate-mannose-protein mannosyltransferase family protein 83, 176
DVU0646 cobI precorrin-2 C20-methyltransferase 23, 176
DVU0648 iron compound ABC transporter ATP-binding protein 23, 176
DVU0649 iron compound ABC transporter permease 23, 176
DVU0650 chelatase 23, 176
DVU0682 DNA-binding protein 141, 229
DVU0726 tgt queuine tRNA-ribosyltransferase 176, 223
DVU0795 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 176, 223
DVU0983 hypothetical protein DVU0983 35, 141
DVU1028 cmk cytidylate kinase 176, 206
DVU1181 response regulator 141, 279
DVU1187 hypothetical protein DVU1187 87, 176
DVU1370 hypothetical protein DVU1370 9, 141
DVU1426 gcvH glycine cleavage system protein H 176, 250
DVU1544 mechanosensitive ion channel family protein 117, 141
DVU1581 hypothetical protein DVU1581 141, 294
DVU1609 dapB dihydrodipicolinate reductase 81, 176
DVU1769 hydA periplasmic 176, 294
DVU1903 mfd transcription-repair coupling factor 176, 334
DVU2142 surE acid phosphatase SurE 176, 198
DVU2209 hypothetical protein DVU2209 176, 278
DVU2302 glutathione-regulated potassium-efflux system protein KefB 141, 277
DVU2315 hypothetical protein DVU2315 162, 176
DVU2330 MRP family protein 35, 141
DVU2338 HhH-GPD family DNA repair protein 117, 141
DVU2413 radical SAM domain-containing protein 141, 185
DVU2425 rarD rarD protein 141, 195
DVU2463 recN DNA repair protein RecN 23, 141
DVU2581 response regulator 141, 278
DVU2780 hypothetical protein DVU2780 69, 141
DVU2899 hypothetical protein DVU2899 141, 316
DVU2900 amidohydrolase family protein 83, 141
DVU2901 pyrB aspartate carbamoyltransferase catalytic subunit 141, 344
DVU2902 pyrC dihydroorotase 141, 278
DVU2932 hypothetical protein DVU2932 117, 141
DVU3008 NeuB family protein 87, 176
DVU3009 radical SAM domain-containing protein 117, 176
DVU3011 hypothetical protein DVU3011 176, 195
DVU3064 sensory box protein 176, 222
DVU3086 cobB-2 cobyrinic acid a,c-diamide synthase 83, 141
DVU3087 cobH precorrin-8X methylmutase 46, 141
DVU3097 outer membrane efflux protein 141, 249
DVU3190 hypothetical protein DVU3190 145, 176
DVU3192 glycosyl transferase group 1 family protein 172, 176
DVU3216 sensor histidine kinase 117, 141
DVU3278 peptidase/PDZ domain-containing protein 83, 141
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 DVU0633
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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