Organism : Bacillus subtilis | Module List :
BSU14100 ykuJ

hypothetical protein (RefSeq)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU14100
(Mouseover regulator name to see its description)

BSU14100 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU14100 ykuJ (22)
Regulator Module Operator
BSU04650 197 tf
BSU05050 197 tf
BSU09510 197 tf
BSU16170 197 tf
BSU23450 197 tf
BSU24520 197 tf
BSU26720 197 tf
BSU37160 197 tf
BSU01810 385 tf
BSU05050 385 tf
BSU10560 385 tf
BSU14990 385 tf
BSU23100 385 tf
BSU23210 385 tf
BSU24320 385 tf
BSU29740 385 tf
BSU36020 385 tf
BSU37080 385 tf
BSU37160 385 tf
BSU38600 385 tf
BSU38700 385 tf
BSU38910 385 tf

Warning: BSU14100 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
5338 9.80e+00 AG.tGgtgAAA
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5339 1.20e+03 CAAGGTCATAGAGCCGTTTTCGAC
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5682 4.90e+01 gcTTtttTtCt
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5683 5.00e+02 AaAaGGaG
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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 BSU14100

BSU14100 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
Module neighborhood information for BSU14100

BSU14100 has total of 44 gene neighbors in modules 197, 385
Gene neighbors (44)
Gene Common Name Description Module membership
BSU00140 dck deoxyadenosine/deoxycytidine kinase (RefSeq) 240, 385
BSU00150 dgk deoxyguanosine kinase (RefSeq) 197, 385
BSU05050 lrpA transcriptional regulator (Lrp/AsnC family) (RefSeq) 197, 255
BSU05470 ydfM putative divalent cation efflux transporter (RefSeq) 132, 197
BSU08930 cspR putative rRNA methylase (RefSeq) 197, 319
BSU12840 pit low-affinity inorganic phosphate transporter (RefSeq) 119, 385
BSU14100 ykuJ hypothetical protein (RefSeq) 197, 385
BSU14110 ykuK putative RNAse (RefSeq) 313, 385
BSU15010 ylbH putative enzyme with adenosyl binding site (RefSeq) 313, 385
BSU15020 coaD phosphopantetheine adenylyltransferase (RefSeq) 313, 385
BSU15450 lspA lipoprotein signal peptidase (RefSeq) 62, 385
BSU15800 thiN thiamine pyrophosphokinase (RefSeq) 197, 385
BSU15820 rpmB 50S ribosomal protein L28 (RefSeq) 119, 197
BSU16680 rpsO 30S ribosomal protein S15 (RefSeq) 119, 197
BSU16950 pbpX penicillin-binding endopeptidase X (RefSeq) 313, 385
BSU19460 yojG putative deacetylase (RefSeq) 197, 354
BSU19620 yodJ D-alanyl-D-alanine carboxypeptidase lipoprotein (RefSeq) 193, 385
BSU21860 yphP hypothetical protein (RefSeq) 197, 309
BSU22190 ypsA hypothetical protein (RefSeq) 382, 385
BSU22370 aspB aspartate aminotransferase (RefSeq) 382, 385
BSU22380 ypmB hypothetical protein (RefSeq) 382, 385
BSU22390 ypmA hypothetical protein (RefSeq) 382, 385
BSU22400 dinG bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon (RefSeq) 227, 385
BSU22440 birA biotin acetyl-CoA-carboxylase ligase and biotin regulon repressor (RefSeq) 382, 385
BSU22600 aroE 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq) 187, 385
BSU22790 hbs non-specific DNA-binding protein HBsu; signal recognition particle-like (SRP) component (RefSeq) 128, 197
BSU24530 yqhM putative lipoate protein ligase (RefSeq) 119, 197
BSU24540 yqhL putative sulfur transferase (RefSeq) 119, 197
BSU24890 yqgN 5-formyltetrahydrofolate cyclo-ligase (RefSeq) 89, 385
BSU24930 yqzD hypothetical protein (RefSeq) 23, 197
BSU24940 yqzC hypothetical protein (RefSeq) 23, 197
BSU25550 rpsT 30S ribosomal protein S20 (RefSeq) 128, 197
BSU29660 rpsD 30S ribosomal protein S4 (RefSeq) 119, 197
BSU31110 yubF hypothetical protein (RefSeq) 23, 197
BSU31120 lytG exoglucosaminidase (RefSeq) 197, 402
BSU33870 yvbI putative permease (RefSeq) 197, 266
BSU36260 ywqC modulator of YwqD protein tyrosine kinase activity (RefSeq) 187, 197
BSU36560 ywnH putative phosphinothricin acetyltransferase (RefSeq) 23, 197
BSU36570 ywnG putative integral inner membrane protein (RefSeq) 23, 197
BSU36900 glyA serine hydroxymethyltransferase (RefSeq) 128, 197
BSU37160 rpoE DNA-directed RNA polymerase subunit delta (RefSeq) 197, 266
BSU38540 dltE putative oxidoreductase (RefSeq) 197, 273
BSU41030 jag SpoIIIJ-associated RNA/ssDNA-binding protein (RefSeq) 313, 385
BSU41040 spoIIIJ OxaA-like protein precursor (RefSeq) 313, 385
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 BSU14100
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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