Organism : Bacillus subtilis | Module List :
BSU34950 pelC

secreted pectate lyase (RefSeq)

CircVis
Functional Annotations (2)
Function System
extracellular region go/ cellular_component
pectate lyase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU34950
(Mouseover regulator name to see its description)

BSU34950 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU34950 pelC (25)
Regulator Module Operator
BSU05370 52 tf
BSU07010 52 tf
BSU09500 52 tf
BSU10880 52 tf
BSU13870 52 tf
BSU25200 52 tf
BSU26220 52 tf
BSU26320 52 tf
BSU33660 52 tf
BSU33670 52 tf
BSU33970 52 tf
BSU36600 52 tf
BSU38450 52 tf
BSU38700 52 tf
BSU40800 52 tf
BSU01430 61 tf
BSU04160 61 tf
BSU05850 61 tf
BSU06140 61 tf
BSU06960 61 tf
BSU09650 61 tf
BSU30260 61 tf
BSU31210 61 tf
BSU35910 61 tf
BSU38700 61 tf

Warning: BSU34950 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
5062 2.00e-10 agAata.aagAaggaaagg.g
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5063 7.80e-01 tcA..atagag.a..gGctGt
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5078 5.80e-07 aatgAAAaCGctTTC
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5079 4.10e+01 aCCccTcC
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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 BSU34950

BSU34950 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
extracellular region go/ cellular_component
pectate lyase activity go/ molecular_function
Module neighborhood information for BSU34950

BSU34950 has total of 48 gene neighbors in modules 52, 61
Gene neighbors (48)
Gene Common Name Description Module membership
BSU04160 mtlR transcriptional regulator (RefSeq) 22, 61
BSU05490 ydfO putative dioxygenase (RefSeq) 52, 178
BSU05500 ydfP putative membrane bound oxidoreductase (RefSeq) 52, 178
BSU06160 gutP H+-glucitol symporter (RefSeq) 61, 326
BSU07800 treP phosphotransferase system (PTS) trehalose-specific enzyme IIBC component (RefSeq) 61, 321
BSU07810 treA trehalose-6-phosphate hydrolase (RefSeq) 61, 321
BSU10870 yisU putative aminoacid related metabolite efflux transporter (RefSeq) 52, 206
BSU11900 yjcL putative integral inner membrane protein; possibly aquaporin-related (RefSeq) 52, 311
BSU11960 yjcR putative phage-related nucleic acid binding terminase small subunit (RefSeq) 52, 342
BSU12000 manR transcriptional antiterminator (RefSeq) 22, 61
BSU12010 manP phosphotransferase system (PTS) mannose-specific enzyme IIBCA component (RefSeq) 61, 168
BSU12020 manA mannose-6 phosphate isomerase ; cupin family (RefSeq) 22, 61
BSU13780 ykvP spore protein (RefSeq) 46, 52
BSU18180 yngB putative UTP-sugar-phosphate uridylyltransferase (RefSeq) 44, 52
BSU19520 yojA putative H+/anion permease (RefSeq) 61, 168
BSU20710 yopZ conserved hypothetical protein; phage SPbeta (RefSeq) 44, 52
BSU24190 yqiI putative N-acetylmuramoyl-L-alanine amidase (RefSeq) 52, 285
BSU24200 yqiH putative lipoprotein (RefSeq) 44, 52
BSU26250 yqaN putative Holliday junction resolvase; skin element (RefSeq) 52, 206
BSU26360 yqaD conserved hypothetical protein; skin element (RefSeq) 52, 129
BSU28730 araQ arabinose/arabinan permease (RefSeq) 61, 250
BSU28750 araN sugar-binding lipoprotein (RefSeq) 61, 250
BSU31040 yuaD hypothetical protein (RefSeq) 61, 334
BSU31180 yulE L-rhamnose isomerase (RefSeq) 61, 330
BSU31190 yulD L-rhamnose mutarotase (RefSeq) 61, 330
BSU31200 yulC rhamnulokinase (RefSeq) 61, 330
BSU31210 yulB putative transcriptional regulator (DeoR family) (RefSeq) 61, 330
BSU31720 degQ pleiotropic regulator (RefSeq) 61, 329
BSU32460 pucM urate oxidase structural factor (RefSeq) 52, 231
BSU32470 pucE xanthine dehydrogenase, iron-sulfur subunit (RefSeq) 52, 326
BSU32480 pucD xanthine dehydrogenase, substrate and molybdenum cofactor subunit (RefSeq) 52, 326
BSU32490 pucC xanthine dehydrogenase, FAD-binding subunit (RefSeq) 52, 326
BSU32890 yusQ putative tautomerase (RefSeq) 52, 389
BSU32900 yusR putative 3-oxoacyl-acyl-carrier protein reductase (RefSeq) 52, 389
BSU32910 yusS putative 3-oxoacyl-acyl-carrier protein reductase (RefSeq) 52, 389
BSU32920 yusT putative transcriptional regulator (LysR family) (RefSeq) 52, 389
BSU32970 yusY hypothetical protein (RefSeq) 31, 52
BSU32980 yusZ short chain dehydrogenase (RefSeq) 52, 285
BSU34670 yvdA putative carbonic anhydrase (RefSeq) 26, 52
BSU34950 pelC secreted pectate lyase (RefSeq) 52, 61
BSU35790 yvyI putative phosphohexomutase ; cupin family (RefSeq) 61, 248
BSU35870 pgsE factor required for polyglutamate synthesis (RefSeq) 44, 61
BSU35890 pgsC capsular polyglutamate amide ligase/translocase subunit (RefSeq) 61, 90
BSU35900 pgsB capsular polyglutamate synthetase (ATP-dependent amide ligase) (RefSeq) 61, 90
BSU38660 yxlF putative ABC transporter component (ATP-binding protein) (RefSeq) 52, 164
BSU39070 bglS endo-beta-1,3-1,4 glucanase (RefSeq) 61, 329
BSU40110 bglA aryl-6-phospho-beta-glucosidase (RefSeq) 61, 318
BSU40560 yybP putative lipoprotein (RefSeq) 52, 178
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 BSU34950
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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