Organism : Bacillus cereus ATCC14579 | Module List :
BC0642

Glutamine transport system permease protein glnP (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
ABC-type amino acid transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
HEQRo_perm_3TM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0642
(Mouseover regulator name to see its description)

BC0642 is regulated by 23 influences and regulates 0 modules.
Regulators for BC0642 (23)
Regulator Module Operator
BC0230 340 tf
BC0477 340 tf
BC0566 340 tf
BC0648 340 tf
BC0680 340 tf
BC2469 340 tf
BC2760 340 tf
BC2964 340 tf
BC3332 340 tf
BC4057 340 tf
BC4525 340 tf
BC4570 340 tf
BC0566 339 tf
BC1851 339 tf
BC2410 339 tf
BC2517 339 tf
BC2680 339 tf
BC2811 339 tf
BC2837 339 tf
BC2964 339 tf
BC3588 339 tf
BC3589 339 tf
BC3903 339 tf

Warning: BC0642 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
4590 5.60e-06 aaAGGgGG
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4591 5.00e+03 GGAGGGA
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4592 4.60e-05 aaaAGgGG
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4593 1.20e+03 agAGGaGGcg
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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 BC0642

BC0642 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type amino acid transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
integral to membrane go/ cellular_component
HEQRo_perm_3TM tigr/ tigrfam
Module neighborhood information for BC0642

BC0642 has total of 36 gene neighbors in modules 339, 340
Gene neighbors (36)
Gene Common Name Description Module membership
BC0203 BC0203 hypothetical protein (NCBI ptt file) 204, 340
BC0309 BC0309 Methyltransferase (NCBI ptt file) 272, 339
BC0401 BC0401 Cystine transport system permease protein (NCBI ptt file) 289, 339
BC0402 BC0402 Cystine-binding protein (NCBI ptt file) 289, 340
BC0557 BC0557 hypothetical protein (NCBI ptt file) 340, 358
BC0558 BC0558 Flottilin (NCBI ptt file) 340, 358
BC0635 BC0635 Spore germination protein KA (NCBI ptt file) 115, 339
BC0638 BC0638 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 339, 407
BC0641 BC0641 Glutamine transport system permease protein glnP (NCBI ptt file) 339, 340
BC0642 BC0642 Glutamine transport system permease protein glnP (NCBI ptt file) 339, 340
BC0847 BC0847 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 340, 405
BC1078 BC1078 Phage infection protein (NCBI ptt file) 54, 339
BC1332 BC1332 None 340, 358
BC2222 BC2222 Oligopeptide transport system permease protein oppB (NCBI ptt file) 253, 339
BC2251 BC2251 Lysine 2,3-aminomutase (NCBI ptt file) 340, 358
BC2252 BC2252 hypothetical Cytosolic Protein (NCBI ptt file) 340, 358
BC2255 BC2255 hypothetical protein (NCBI ptt file) 272, 340
BC2300 BC2300 Oxalate/formate antiporter (NCBI ptt file) 327, 340
BC2651 BC2651 hypothetical protein (NCBI ptt file) 291, 339
BC2678 BC2678 hypothetical protein (NCBI ptt file) 339, 459
BC2682 BC2682 Chitosanase (NCBI ptt file) 293, 340
BC2875 BC2875 hypothetical protein (NCBI ptt file) 334, 339
BC2972 BC2972 hypothetical protein (NCBI ptt file) 339, 397
BC2999 BC2999 hypothetical Membrane Spanning Protein (NCBI ptt file) 13, 340
BC3076 BC3076 Acetyltransferase (NCBI ptt file) 189, 340
BC3357 BC3357 hypothetical protein (NCBI ptt file) 186, 339
BC3516 BC3516 CDP-abequose synthase (NCBI ptt file) 162, 339
BC3612 BC3612 Thiol:disulfide interchange protein tlpA (NCBI ptt file) 232, 340
BC3733 BC3733 hypothetical protein (NCBI ptt file) 334, 339
BC3751 BC3751 hypothetical protein (NCBI ptt file) 334, 339
BC3928 BC3928 hypothetical Membrane Spanning Protein (NCBI ptt file) 131, 339
BC3959 BC3959 hypothetical protein (NCBI ptt file) 84, 340
BC4407 BC4407 Stage V sporulation protein B (NCBI ptt file) 17, 339
BC4607 BC4607 hypothetical protein (NCBI ptt file) 217, 339
BC5217 BC5217 PTS system, lichenan oligosaccharide-specific IIB component (NCBI ptt file) 199, 339
BC5252 BC5252 hypothetical Membrane Spanning Protein (NCBI ptt file) 327, 340
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 BC0642
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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