Organism : Bacillus subtilis | Module List :
BSU07450 yfmJ

putative oxidoreductase (RefSeq)

CircVis
Functional Annotations (5)
Function System
Putative NADP-dependent oxidoreductases cog/ cog
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
carbohydrate metabolic process go/ biological_process
zinc ion binding go/ molecular_function
oxidoreductase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU07450
(Mouseover regulator name to see its description)

BSU07450 is regulated by 27 influences and regulates 0 modules.
Regulators for BSU07450 yfmJ (27)
Regulator Module Operator
BSU00330 90 tf
BSU02680 90 tf
BSU04820 90 tf
BSU05270 90 tf
BSU05670 90 tf
BSU09990 90 tf
BSU13870 90 tf
BSU20780 90 tf
BSU25200 90 tf
BSU27520 90 tf
BSU29690 90 tf
BSU35490 90 tf
BSU35650 90 tf
BSU36110 90 tf
BSU39990 90 tf
BSU40970 90 tf
BSU00470 359 tf
BSU00800 359 tf
BSU08990 359 tf
BSU09380 359 tf
BSU10860 359 tf
BSU15970 359 tf
BSU16600 359 tf
BSU19090 359 tf
BSU33080 359 tf
BSU35050 359 tf
BSU36020 359 tf

Warning: BSU07450 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
5134 1.60e+01 AgGAGagg
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5135 2.10e+02 AaaacGaAagaGctt
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5642 3.80e-06 AaAGGaGGaa
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5643 3.10e+04 CCGCCCaACTC
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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 BSU07450

BSU07450 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Putative NADP-dependent oxidoreductases cog/ cog
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
carbohydrate metabolic process go/ biological_process
zinc ion binding go/ molecular_function
oxidoreductase activity go/ molecular_function
Module neighborhood information for BSU07450

BSU07450 has total of 49 gene neighbors in modules 90, 359
Gene neighbors (49)
Gene Common Name Description Module membership
BSU01560 kbaA inner membrane protein involved in activation of the KinB signaling pathway to sporulation (RefSeq) 31, 359
BSU03410 bglC aryl-phospho-beta-d-glucosidase (RefSeq) 90, 217
BSU03480 srfAA surfactin synthetase (RefSeq) 90, 353
BSU03490 srfAB surfactin synthetase (RefSeq) 90, 353
BSU03500 comS regulator of genetic competence (RefSeq) 90, 353
BSU03510 srfAC surfactin synthetase (RefSeq) 90, 353
BSU03520 srfAD surfactin synthetase (RefSeq) 90, 353
BSU03770 rapC response regulator aspartate phosphatase (RefSeq) 90, 353
BSU03990 mtlD mannitol-1-phosphate 5-dehydrogenase (RefSeq) 90, 330
BSU06140 gutR transcriptional regulator of the glucitol operon (RefSeq) 26, 359
BSU06240 test acetoin reductase/2,3-butanediol dehydrogenase (RefSeq) 90, 340
BSU07450 yfmJ putative oxidoreductase (RefSeq) 90, 359
BSU07530 yfmB hypothetical protein (RefSeq) 222, 359
BSU07540 yfmA hypothetical protein (RefSeq) 222, 359
BSU08470 yfhB putative isomerase (RefSeq) 90, 353
BSU10210 yhfF hypothetical protein (RefSeq) 90, 101
BSU11540 pepF oligoendopeptidase F (RefSeq) 90, 412
BSU13990 kinA sporulation-specific ATP-dependent protein histidine kinase (RefSeq) 205, 359
BSU14220 ykuU putative 2-cys peroxiredoxin (RefSeq) 91, 359
BSU14230 ykuV thiol-disulfide isomerase (RefSeq) 91, 359
BSU17240 ymzB hypothetical protein (RefSeq) 165, 359
BSU17250 ymaE putative hydrolase (RefSeq) 114, 359
BSU17340 hfq RNA-binding protein Hfq (RefSeq) 95, 359
BSU18630 exlX extracellular endoglucanase precursor (expansin) (RefSeq) 25, 90
BSU19400 sodC superoxide dismutase (exported lipoprotein) (RefSeq) 239, 359
BSU26820 yrpD putative lipoprotein (RefSeq) 25, 359
BSU29540 ppnK inorganic polyphosphate/ATP-NAD kinase (RefSeq) 77, 359
BSU29670 tyrS tyrosyl-tRNA synthetase (RefSeq) 90, 340
BSU31690 comP two-component sensor histidine kinase (RefSeq) 90, 340
BSU31700 comX competence pheromone precursor (pheromone peptide aa 46->55, modified) (RefSeq) 90, 340
BSU31930 ald L-alanine dehydrogenase (RefSeq) 90, 256
BSU32990 mrgA metalloregulation DNA-binding stress protein (RefSeq) 296, 359
BSU33540 yvaB azoreductase (RefSeq) 90, 353
BSU34390 pnbA para-nitrobenzyl esterase (intracellular esterase B) (RefSeq) 353, 359
BSU34630 mdxR putative transcriptional regulator (LacI family) (RefSeq) 90, 318
BSU35890 pgsC capsular polyglutamate amide ligase/translocase subunit (RefSeq) 61, 90
BSU35900 pgsB capsular polyglutamate synthetase (ATP-dependent amide ligase) (RefSeq) 61, 90
BSU37220 ywjB putative oxidoreductase (RefSeq) 359, 391
BSU37230 ywjA putative ABC lipid transporter (ATP-binding protein) (RefSeq) 359, 391
BSU38040 sacA sucrase-6-phosphate hydrolase (RefSeq) 248, 359
BSU38770 cimH citrate/malate/H+ symporter (RefSeq) 329, 359
BSU39090 yxiP putative lipoprotein (RefSeq) 90, 91
BSU39100 yxiO putative efflux transporter (RefSeq) 215, 359
BSU39820 htpG heat shock protein 90 (RefSeq) 90, 229
BSU39870 yxbD putative acetyltransferase (RefSeq) 25, 359
BSU40180 yydF peptide controlling LiaRS (RefSeq) 114, 359
BSU40460 yyzB hypothetical protein (RefSeq) 359, 387
BSU40820 yyaL hypothetical protein (RefSeq) 81, 359
VIMSS39309 VIMSS39309 None 90, 191
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 BSU07450
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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