Organism : Bacillus subtilis | Module List :
BSU01220 rpsC

30S ribosomal protein S3 (RefSeq)

CircVis
Functional Annotations (7)
Function System
Ribosomal protein S3 cog/ cog
RNA binding go/ molecular_function
structural constituent of ribosome go/ molecular_function
translation go/ biological_process
small ribosomal subunit go/ cellular_component
Ribosome kegg/ kegg pathway
rpsC_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU01220
(Mouseover regulator name to see its description)

BSU01220 is regulated by 14 influences and regulates 0 modules.
Regulators for BSU01220 rpsC (14)
Regulator Module Operator
BSU00470 76 tf
BSU01070 76 tf
BSU01080 76 tf
BSU01430 76 tf
BSU09650 76 tf
BSU16600 76 tf
BSU29630 76 tf
BSU30020 76 tf
BSU36020 76 tf
BSU01080 196 tf
BSU01430 196 tf
BSU04100 196 tf
BSU09270 196 tf
BSU29630 196 tf

Warning: BSU01220 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

Warning: No Motifs were found!

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 BSU01220

BSU01220 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Ribosomal protein S3 cog/ cog
RNA binding go/ molecular_function
structural constituent of ribosome go/ molecular_function
translation go/ biological_process
small ribosomal subunit go/ cellular_component
Ribosome kegg/ kegg pathway
rpsC_bact tigr/ tigrfam
Module neighborhood information for BSU01220

BSU01220 has total of 22 gene neighbors in modules 76, 196
Gene neighbors (22)
Gene Common Name Description Module membership
BSU01150 rpsJ 30S ribosomal protein S10 (RefSeq) 76, 112
BSU01160 rplC 50S ribosomal protein L3 (RefSeq) 76, 112
BSU01170 rplD 50S ribosomal protein L4 (RefSeq) 76, 112
BSU01180 rplW 50S ribosomal protein L23 (RefSeq) 76, 112
BSU01190 rplB 50S ribosomal protein L2 (RefSeq) 76, 112
BSU01200 rpsS 30S ribosomal protein S19 (RefSeq) 76, 112
BSU01210 rplV 50S ribosomal protein L22 (RefSeq) 76, 112
BSU01220 rpsC 30S ribosomal protein S3 (RefSeq) 76, 196
BSU01230 rplP 50S ribosomal protein L16 (RefSeq) 76, 196
BSU01240 rpmC 50S ribosomal protein L29 (RefSeq) 76, 196
BSU01250 rpsQ 30S ribosomal protein S17 (RefSeq) 76, 196
BSU01260 rplN 50S ribosomal protein L14 (RefSeq) 76, 196
BSU01270 rplX 50S ribosomal protein L24 (RefSeq) 140, 196
BSU01280 rplE 50S ribosomal protein L5 (RefSeq) 76, 196
BSU01290 rpsN 30S ribosomal protein S14 (RefSeq) 140, 196
BSU01300 rpsH 30S ribosomal protein S8 (RefSeq) 140, 196
BSU01310 rplF 50S ribosomal protein L6 (RefSeq) 76, 196
BSU01320 rplR 50S ribosomal protein L18 (RefSeq) 140, 196
BSU01330 rpsE 30S ribosomal protein S5 (RefSeq) 140, 196
BSU01340 rpmD 50S ribosomal protein L30 (RefSeq) 140, 196
BSU01350 rplO 50S ribosomal protein L15 (RefSeq) 140, 196
BSU01370 adk adenylate kinase (RefSeq) 140, 196
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 BSU01220
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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