Organism : Bacillus subtilis | Module List :
VIMSS39966

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VIMSS39966
(Mouseover regulator name to see its description)

VIMSS39966 is regulated by 21 influences and regulates 0 modules.
Regulators for VIMSS39966 (21)
Regulator Module Operator
BSU00700 25 tf
BSU01640 25 tf
BSU02220 25 tf
BSU10560 25 tf
BSU10860 25 tf
BSU24250 25 tf
BSU24610 25 tf
BSU29630 25 tf
BSU30150 25 tf
BSU35050 25 tf
BSU37620 25 tf
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

Warning: VIMSS39966 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
5012 5.00e-04 aaAGGaGG
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5013 8.60e+03 TTttttCAtaA
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5422 3.20e+01 cGcgcCcG
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5423 1.40e+04 cGgaAgGa
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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 VIMSS39966

Warning: No Functional annotations were found!

Module neighborhood information for VIMSS39966

VIMSS39966 has total of 48 gene neighbors in modules 25, 240
Gene neighbors (48)
Gene Common Name Description Module membership
BSU00140 dck deoxyadenosine/deoxycytidine kinase (RefSeq) 240, 385
BSU00490 spoVG regulatory protein SpoVG (RefSeq) 25, 353
BSU01600 ybbA putative iron-chelator esterase (RefSeq) 25, 65
BSU01610 feuC iron-uptake protein (RefSeq) 25, 65
BSU01640 ybbB putative transcriptional regulator (AraC/XylS family) (RefSeq) 25, 65
BSU02040 ybdN hypothetical protein (RefSeq) 25, 141
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
BSU10340 phoE phosphatase (RefSeq) 28, 240
BSU10730 yisI Spo0A-P phosphatase (RefSeq) 25, 215
BSU11820 yjcD putative ATP-dependent DNA helicase (RefSeq) 240, 325
BSU11990 yjdB hypothetical protein (RefSeq) 25, 91
BSU12450 yjpA putative enzyme (RefSeq) 25, 404
BSU14120 ykzF hypothetical protein (RefSeq) 25, 350
BSU14940 ylbA hypothetical protein (RefSeq) 25, 404
BSU17100 pksC malonyl-CoA-acyltransferase involved in polyketide synthesis (RefSeq) 25, 91
BSU18630 exlX extracellular endoglucanase precursor (expansin) (RefSeq) 25, 90
BSU18780 yoaW biofilm forming exported protein (RefSeq) 25, 114
BSU21670 BSU21670 None 25, 159
BSU22280 yppD hypothetical protein (RefSeq) 25, 33
BSU24600 sinI antagonist of SinR (RefSeq) 25, 302
BSU24800 yqgW hypothetical protein (RefSeq) 25, 404
BSU25840 phrE regulator of the activity of phosphatase RapE (RefSeq) 25, 114
BSU26230 yqaP conserved hypothetical protein; skin element (RefSeq) 25, 64
BSU26820 yrpD putative lipoprotein (RefSeq) 25, 359
BSU27160 cypB cytochrome P450 CYP102A3 (RefSeq) 50, 240
BSU27170 bscR transcriptional regulator for cypB (RefSeq) 50, 240
BSU31510 yufK putative integral inner membrane protein (RefSeq) 132, 240
BSU35050 yvnA putative transcriptional regulator (RefSeq) 25, 91
BSU36360 mscL large-conductance mechanosensitive channel (RefSeq) 1, 240
BSU37030 racA polar chromosome segregation protein (RefSeq) 25, 114
BSU37800 yweA member of the processed secretome (RefSeq) 25, 91
BSU39870 yxbD putative acetyltransferase (RefSeq) 25, 359
BSU40670 yybE putative transcriptional regulator (LysR family) (RefSeq) 11, 240
BSU40680 yybD putative acetyltransferase (RefSeq) 11, 240
VIMSS38533 VIMSS38533 None 235, 240
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 VIMSS39966
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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