Organism : Bacillus subtilis | Module List :
BSU11820 yjcD

putative ATP-dependent DNA helicase (RefSeq)

CircVis
Functional Annotations (7)
Function System
Superfamily I DNA and RNA helicases cog/ cog
DNA binding go/ molecular_function
ATP-dependent DNA helicase activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
Nucleotide excision repair kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU11820
(Mouseover regulator name to see its description)

BSU11820 is regulated by 16 influences and regulates 0 modules.
Regulators for BSU11820 yjcD (16)
Regulator Module Operator
BSU02370 240 tf
BSU03850 240 tf
BSU04060 240 tf
BSU04100 240 tf
BSU10560 240 tf
BSU15330 240 tf
BSU27170 240 tf
BSU30460 240 tf
BSU38910 240 tf
BSU40670 240 tf
BSU01010 325 tf
BSU15970 325 tf
BSU16600 325 tf
BSU24320 325 tf
BSU33740 325 tf
BSU36020 325 tf

Warning: BSU11820 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5422 3.20e+01 cGcgcCcG
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5423 1.40e+04 cGgaAgGa
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5588 1.60e+01 ta.ATaa.gggGAta
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5589 4.90e+02 CCTTTtTtatt
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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 BSU11820

BSU11820 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Superfamily I DNA and RNA helicases cog/ cog
DNA binding go/ molecular_function
ATP-dependent DNA helicase activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
Nucleotide excision repair kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Module neighborhood information for BSU11820

BSU11820 has total of 47 gene neighbors in modules 240, 325
Gene neighbors (47)
Gene Common Name Description Module membership
BSU00140 dck deoxyadenosine/deoxycytidine kinase (RefSeq) 240, 385
BSU00500 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase (RefSeq) 292, 325
BSU00510 prs ribose-phosphate pyrophosphokinase (RefSeq) 292, 325
BSU02350 nagP phosphotransferase system (PTS) glucosamine-specific enzyme IICBA component (RefSeq) 24, 240
BSU02360 nagBB glucosamine-6-phosphate isomerase (RefSeq) 24, 240
BSU02400 ybgF putative aminoacid permease (RefSeq) 199, 240
BSU03840 ycnB putative efflux transporter (RefSeq) 13, 240
BSU04050 ycsF LamB/YcsF family protein (RefSeq) 176, 240
BSU04060 ycsG putative branched chain amino acids transporter (RefSeq) 176, 240
BSU04070 ycsI hypothetical protein (RefSeq) 176, 240
BSU04080 kipI putative inhibitor of the autophosphorylation reaction of KinA (RefSeq) 176, 240
BSU04090 kipA putative hydrolase subunit antagonist of KipI (RefSeq) 176, 240
BSU04100 kipR transcriptional regulator (IclR family) (RefSeq) 176, 240
BSU04500 ydbK putative efflux ABC-transporter (permease component) (RefSeq) 89, 240
BSU06812 BSU06812 None 120, 240
BSU08350 estB secreted esterase / lipase (RefSeq) 240, 339
BSU08450 yfiZ iron(III) siderophore transport permease (RefSeq) 93, 325
BSU08460 yfhA iron(III) siderophore transport permease (RefSeq) 93, 325
BSU09120 yhcK putative diguanylate cyclase or phosphodiesterase (RefSeq) 190, 325
BSU10340 phoE phosphatase (RefSeq) 28, 240
BSU11820 yjcD putative ATP-dependent DNA helicase (RefSeq) 240, 325
BSU15970 ylxM putative DNA-binding protein (RefSeq) 212, 325
BSU15980 ffh signal recognition particle-like (SRP) GTPase (RefSeq) 212, 325
BSU16530 uppS undecaprenyl pyrophosphate synthase (RefSeq) 325, 343
BSU27160 cypB cytochrome P450 CYP102A3 (RefSeq) 50, 240
BSU27170 bscR transcriptional regulator for cypB (RefSeq) 50, 240
BSU30530 ytnA putative amino acid permease (RefSeq) 79, 325
BSU30540 asnB asparagine synthetase (RefSeq) 62, 325
BSU30550 metK S-adenosylmethionine synthetase (RefSeq) 325, 374
BSU31510 yufK putative integral inner membrane protein (RefSeq) 132, 240
BSU34690 yvcS putative ABC transporter (permease) (RefSeq) 73, 325
BSU34700 yvcR putative ABC transporter (ATP-binding protein) (RefSeq) 325, 339
BSU34710 yvcQ two-component sensor histidine kinase [YvcP] (RefSeq) 202, 325
BSU34720 yvcP two-component response regulator [YvcQ] (RefSeq) 325, 339
BSU36360 mscL large-conductance mechanosensitive channel (RefSeq) 1, 240
BSU36410 mbl rod shape-determining protein Mbl (RefSeq) 62, 325
BSU36760 murAA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (RefSeq) 170, 325
BSU36770 ywmB hypothetical protein (RefSeq) 172, 325
BSU36780 ywzB hypothetical protein (RefSeq) 172, 325
BSU36880 atpI ATP synthase (subunit i) (RefSeq) 172, 325
BSU36890 upp uracil phosphoribosyltransferase (RefSeq) 292, 325
BSU38520 dltC D-alanine--poly(phosphoribitol) ligase subunit 2 (RefSeq) 172, 325
BSU40670 yybE putative transcriptional regulator (LysR family) (RefSeq) 11, 240
BSU40680 yybD putative acetyltransferase (RefSeq) 11, 240
VIMSS38533 VIMSS38533 None 235, 240
VIMSS39424 VIMSS39424 None 293, 325
VIMSS39966 VIMSS39966 None 25, 240
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 BSU11820
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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