Organism : Bacillus cereus ATCC14579 | Module List :
BC4902

Transcriptional regulator, AsnC family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4902
(Mouseover regulator name to see its description)

BC4902 is regulated by 24 influences and regulates 17 modules.
Regulators for BC4902 (24)
Regulator Module Operator
BC0051 175 tf
BC0116 175 tf
BC0230 175 tf
BC3814 175 tf
BC3976 175 tf
BC4902 175 tf
BC4930 175 tf
BC5024 175 tf
BC5250 175 tf
BC5339 175 tf
BC0607 455 tf
BC0648 455 tf
BC0954 455 tf
BC1302 455 tf
BC1710 455 tf
BC3320 455 tf
BC3332 455 tf
BC3653 455 tf
BC4181 455 tf
BC4294 455 tf
BC5074 455 tf
BC5352 455 tf
BC5368 455 tf
BC5373 455 tf

Warning: BC4902 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
4266 4.50e+03 GcaaGatgAATtgcGc
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4267 6.20e+03 CaGCTGCC
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4820 3.50e-39 ATAAAGTGAAACTTTAATCAGtgG
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4821 1.50e-11 GagTctTACTgCCCataAATgcgg
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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 BC4902

BC4902 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC4902

BC4902 has total of 41 gene neighbors in modules 175, 455
Gene neighbors (41)
Gene Common Name Description Module membership
BC0188 BC0188 Phosphoglucosamine mutase (NCBI ptt file) 394, 455
BC0189 BC0189 hypothetical protein (NCBI ptt file) 175, 263
BC0417 BC0417 DNA topoisomerase I (NCBI ptt file) 235, 455
BC0463 BC0463 hypothetical protein (NCBI ptt file) 96, 175
BC0469 BC0469 None 161, 455
BC0510 BC0510 Integral membrane protein (NCBI ptt file) 319, 455
BC0541 BC0541 Monofunctional biosynthetic peptidoglycan transglycosylase (NCBI ptt file) 18, 455
BC0933 BC0933 hypothetical protein (NCBI ptt file) 141, 175
BC1198 BC1198 GTP pyrophosphokinase (NCBI ptt file) 455, 513
BC1203 BC1203 Cell division protein ftsW (NCBI ptt file) 130, 455
BC1302 BC1302 Transcriptional regulator, GntR family (NCBI ptt file) 439, 455
BC1303 BC1303 (S)-2-hydroxy-acid oxidase, iron-sulfur chain (NCBI ptt file) 235, 455
BC1304 BC1304 iron-sulfur cluster-binding protein (NCBI ptt file) 235, 455
BC1305 BC1305 hypothetical protein (NCBI ptt file) 235, 455
BC1506 BC1506 hypothetical protein (NCBI ptt file) 26, 175
BC2020 BC2020 Spermine/spermidine acetyltransferase (NCBI ptt file) 175, 225
BC2715 BC2715 hypothetical Membrane Spanning Protein (NCBI ptt file) 139, 175
BC2949 BC2949 hypothetical Membrane Spanning Protein (NCBI ptt file) 130, 455
BC3201 BC3201 Two component system histidine kinase (NCBI ptt file) 6, 455
BC3487 BC3487 hypothetical protein (NCBI ptt file) 175, 209
BC3501 BC3501 Response regulator aspartate phosphatase (NCBI ptt file) 175, 197
BC3602 BC3602 Anaerobic ribonucleoside-triphosphate reductase activating protein (NCBI ptt file) 175, 475
BC3635 BC3635 hypothetical protein (NCBI ptt file) 47, 175
BC3664 BC3664 N-acyl-L-amino acid amidohydrolase (NCBI ptt file) 15, 455
BC3774 BC3774 Pyruvate synthase alpha chain (NCBI ptt file) 371, 455
BC4248 BC4248 hypothetical protein (NCBI ptt file) 235, 455
BC4260 BC4260 Glucokinase (NCBI ptt file) 72, 175
BC4293 BC4293 hypothetical Cytosolic Protein (NCBI ptt file) 371, 455
BC4294 BC4294 CBS domain containing protein (NCBI ptt file) 371, 455
BC4359 BC4359 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 235, 455
BC4495 BC4495 Germination protein germ (NCBI ptt file) 449, 455
BC4572 BC4572 hypothetical Cytosolic Protein (NCBI ptt file) 263, 455
BC4597 BC4597 hypothetical Membrane Spanning Protein (NCBI ptt file) 235, 455
BC4682 BC4682 IAA acetyltransferase (NCBI ptt file) 137, 175
BC4683 BC4683 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 137, 175
BC4798 BC4798 hypothetical protein (NCBI ptt file) 235, 455
BC4799 BC4799 hypothetical protein (NCBI ptt file) 235, 455
BC4800 BC4800 surface protein (NCBI ptt file) 235, 455
BC4857 BC4857 1,4-dihydroxy-2-naphthoate octaprenyltransferase (NCBI ptt file) 403, 455
BC4902 BC4902 Transcriptional regulator, AsnC family (NCBI ptt file) 175, 455
BC4903 BC4903 Gluconate 2-dehydrogenase (NCBI ptt file) 302, 455
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 BC4902
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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