Organism : Bacillus cereus ATCC14579 | Module List :
BC3400

RRF2 family protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulator cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3400
(Mouseover regulator name to see its description)

BC3400 is regulated by 14 influences and regulates 16 modules.
Regulators for BC3400 (14)
Regulator Module Operator
BC0518 501 tf
BC0595 501 tf
BC0657 501 tf
BC1296 501 tf
BC1710 501 tf
BC3400 501 tf
BC5038 501 tf
BC0518 247 tf
BC0595 247 tf
BC0657 247 tf
BC1296 247 tf
BC1710 247 tf
BC3400 247 tf
BC5038 247 tf

Warning: BC3400 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
4410 8.60e+02 GCtgCTTgCgCTT
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4411 3.50e+03 GAGGTG
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4912 1.30e+01 aacaAaagGaG
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4913 2.80e+03 ATtTCACtat..GtTCaC
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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 BC3400

BC3400 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulator cog/ cog
Module neighborhood information for BC3400

BC3400 has total of 31 gene neighbors in modules 247, 501
Gene neighbors (31)
Gene Common Name Description Module membership
BC0518 BC0518 Peroxide operon regulator (NCBI ptt file) 247, 335
BC0657 BC0657 Transcriptional regulator, MarR family (NCBI ptt file) 247, 501
BC0658 BC0658 Multidrug resistance protein B (NCBI ptt file) 247, 501
BC1154 BC1154 Ferrochelatase (NCBI ptt file) 247, 501
BC1155 BC1155 Catalase (NCBI ptt file) 247, 501
BC1161 BC1161 Peptidyl-prolyl cis-trans isomerase (NCBI ptt file) 247, 501
BC1296 BC1296 (S)-2-hydroxy-acid oxidase subunit GlcF (NCBI ptt file) 247, 335
BC1297 BC1297 (S)-2-hydroxy-acid oxidase chain D (NCBI ptt file) 247, 501
BC1461 BC1461 DNA integration/recombination/invertion protein (NCBI ptt file) 247, 501
BC1827 BC1827 hypothetical Cytosolic Protein (NCBI ptt file) 247, 501
BC2194 BC2194 FMN-dependent NADH-azoreductase (NCBI ptt file) 247, 501
BC3223 BC3223 ABC transporter permease protein (NCBI ptt file) 247, 501
BC3399 BC3399 hypothetical protein (NCBI ptt file) 247, 501
BC3400 BC3400 RRF2 family protein (NCBI ptt file) 247, 501
BC3401 BC3401 hypothetical protein (NCBI ptt file) 247, 501
BC3402 BC3402 Arsenate reductase family protein (NCBI ptt file) 247, 501
BC3600 BC3600 Protease HhoA (NCBI ptt file) 247, 501
BC3925 BC3925 None 103, 247
BC4263 BC4263 LSU ribosomal protein L33P (NCBI ptt file) 74, 501
BC4341 BC4341 GTP pyrophosphokinase (NCBI ptt file) 247, 501
BC4748 BC4748 ABC transporter ATP-binding protein (NCBI ptt file) 15, 501
BC4797 BC4797 hypothetical protein (NCBI ptt file) 119, 501
BC4989 BC4989 Thioredoxin (NCBI ptt file) 247, 501
BC4990 BC4990 DNA primase (bacterial type) and small primase-like proteins (NCBI ptt file) 247, 501
BC5037 BC5037 Pirin (NCBI ptt file) 247, 501
BC5038 BC5038 Transcriptional regulator, MarR family (NCBI ptt file) 247, 501
BC5044 BC5044 Non-specific DNA-binding protein Dps / Iron-binding ferritin-like antioxidant protein / Ferroxidase (NCBI ptt file) 247, 501
BC5059 BC5059 Transcriptional regulator, MarR family (NCBI ptt file) 247, 501
BC5132 BC5132 Murein hydrolase export regulator (NCBI ptt file) 247, 501
BC5133 BC5133 Murein hydrolase exporter (NCBI ptt file) 247, 501
BC5174 BC5174 hypothetical Membrane Spanning Protein (NCBI ptt file) 354, 501
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 BC3400
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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