Organism : Bacillus cereus ATCC14579 | Module List :
BC3428

Lysine exporter protein (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Putative threonine efflux protein cog/ cog
amino acid transport go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3428
(Mouseover regulator name to see its description)

BC3428 is regulated by 24 influences and regulates 0 modules.
Regulators for BC3428 (24)
Regulator Module Operator
BC0114 257 tf
BC0607 257 tf
BC0854 257 tf
BC1363 257 tf
BC1427 257 tf
BC1841 257 tf
BC1987 257 tf
BC2401 257 tf
BC2514 257 tf
BC3207 257 tf
BC3826 257 tf
BC4010 257 tf
BC5143 257 tf
BC0518 256 tf
BC1531 256 tf
BC1673 256 tf
BC2401 256 tf
BC2672 256 tf
BC2979 256 tf
BC3982 256 tf
BC4010 256 tf
BC4256 256 tf
BC4501 256 tf
BC4650 256 tf

Warning: BC3428 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
4428 3.20e-08 gtataaAa.AgaGagGgaa
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4429 7.80e+03 GGGCGG
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4430 5.50e+00 AAgGAGg
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4431 1.10e+04 gAtgAAGAGGaGC
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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 BC3428

BC3428 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Putative threonine efflux protein cog/ cog
amino acid transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for BC3428

BC3428 has total of 51 gene neighbors in modules 256, 257
Gene neighbors (51)
Gene Common Name Description Module membership
BC0014 BC0014 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 257, 461
BC0022 BC0022 Pyrazinamidase (NCBI ptt file) 9, 256
BC0564 BC0564 hypothetical lipoprotein (NCBI ptt file) 245, 257
BC0579 BC0579 Malate-sodium symport (NCBI ptt file) 234, 257
BC0674 BC0674 Permease (NCBI ptt file) 257, 465
BC0676 BC0676 hypothetical protein (NCBI ptt file) 257, 308
BC0803 BC0803 Sodium-dependent phosphate transporter (NCBI ptt file) 257, 388
BC0812 BC0812 PBS lyase HEAT-like repeat (NCBI ptt file) 62, 256
BC0826 BC0826 hypothetical DNA-binding protein (NCBI ptt file) 141, 257
BC0879 BC0879 hypothetical Membrane Associated Protein (NCBI ptt file) 257, 449
BC0932 BC0932 hypothetical protein (NCBI ptt file) 256, 453
BC0941 BC0941 Type II restriction-modification system methylation subunit (NCBI ptt file) 257, 343
BC1042 BC1042 hypothetical Cytosolic Protein (NCBI ptt file) 10, 256
BC1217 BC1217 hypothetical protein (NCBI ptt file) 256, 479
BC1284 BC1284 Immune inhibitor A precursor (NCBI ptt file) 256, 400
BC1319 BC1319 Oxidoreductase (NCBI ptt file) 257, 449
BC1427 BC1427 CbiX protein (NCBI ptt file) 165, 257
BC1455 BC1455 Multimodular transpeptidase-transglycosylase PBP 2A (NCBI ptt file) 223, 256
BC1462 BC1462 None 256, 468
BC1578 BC1578 hypothetical protein (NCBI ptt file) 243, 256
BC1579 BC1579 putative synthetase/amidase (NCBI ptt file) 67, 256
BC1580 BC1580 surface protein (NCBI ptt file) 67, 256
BC1617 BC1617 hypothetical Cytosolic Protein (NCBI ptt file) 257, 443
BC1704 BC1704 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 230, 256
BC1796 BC1796 hypothetical protein (NCBI ptt file) 256, 421
BC2061 BC2061 Multidrug resistance protein B (NCBI ptt file) 256, 428
BC2374 BC2374 hypothetical Membrane Spanning Protein (NCBI ptt file) 257, 281
BC2401 BC2401 Transcriptional regulator, MarR family (NCBI ptt file) 222, 256
BC2554 BC2554 hypothetical protein (NCBI ptt file) 257, 432
BC2557 BC2557 Prophage helix-turn-helix protein (NCBI ptt file) 62, 256
BC2688 BC2688 Penicillin-binding protein (NCBI ptt file) 254, 256
BC2799 BC2799 Macrolide glycosyltransferase (NCBI ptt file) 254, 256
BC2894 BC2894 Macrolide-efflux protein (NCBI ptt file) 257, 343
BC3110 BC3110 Spore germination protein BC (NCBI ptt file) 10, 256
BC3135 BC3135 Carboxymethylenebutenolidase-related protein (NCBI ptt file) 256, 460
BC3227 BC3227 Two component system histidine kinase (NCBI ptt file) 55, 256
BC3428 BC3428 Lysine exporter protein (NCBI ptt file) 256, 257
BC3775 BC3775 Microsomal dipeptidase (NCBI ptt file) 257, 312
BC3785 BC3785 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 256, 288
BC4088 BC4088 IG hypothetical 17224 (NCBI ptt file) 257, 414
BC4275 BC4275 hypothetical protein (NCBI ptt file) 257, 461
BC4295 BC4295 DNA repair protein recO (NCBI ptt file) 252, 257
BC4439 BC4439 Ribonuclease G (NCBI ptt file) 256, 308
BC4466 BC4466 CotS-related protein (NCBI ptt file) 256, 517
BC4511 BC4511 Acid phosphatase (NCBI ptt file) 221, 257
BC4535 BC4535 Bacitracin transport permease protein BCRB (NCBI ptt file) 250, 256
BC4688 BC4688 hypothetical protein (NCBI ptt file) 257, 313
BC4715 BC4715 Glucose 1-dehydrogenase (NCBI ptt file) 150, 256
BC4761 BC4761 S-adenosylmethionine synthetase (NCBI ptt file) 134, 257
BC5193 BC5193 COMF operon protein 1 (NCBI ptt file) 67, 257
BC5370 BC5370 Agmatinase (NCBI ptt file) 257, 382
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 BC3428
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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