Organism : Bacillus cereus ATCC14579 | Module List :
BC5141

Central glycolytic genes regulator (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator, contains sigma factor-related N-terminal domain cog/ cog
carbohydrate binding go/ molecular_function
transcription regulator activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5141
(Mouseover regulator name to see its description)

BC5141 is regulated by 26 influences and regulates 16 modules.
Regulators for BC5141 (26)
Regulator Module Operator
BC0042 188 tf
BC0122 188 tf
BC0158 188 tf
BC0265 188 tf
BC0806 188 tf
BC1075 188 tf
BC1387 188 tf
BC1841 188 tf
BC3128 188 tf
BC3253 188 tf
BC3706 188 tf
BC3976 188 tf
BC4708 188 tf
BC4842 188 tf
BC5141 188 tf
BC0042 70 tf
BC0123 70 tf
BC0158 70 tf
BC0265 70 tf
BC1296 70 tf
BC1936 70 tf
BC2358 70 tf
BC3539 70 tf
BC4670 70 tf
BC4859 70 tf
BC5141 70 tf

Warning: BC5141 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
4060 1.50e-01 aagaGGaaaag
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4061 7.30e+01 GataaataGa.AaagAaaGcG
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4292 2.00e+00 gCcaa.gAAAGcG
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4293 2.60e+02 ggaCatacagacAtg
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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 BC5141

BC5141 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator, contains sigma factor-related N-terminal domain cog/ cog
carbohydrate binding go/ molecular_function
transcription regulator activity go/ molecular_function
Module neighborhood information for BC5141

BC5141 has total of 29 gene neighbors in modules 70, 188
Gene neighbors (29)
Gene Common Name Description Module membership
BC0128 BC0128 Protein Translation Elongation Factor G (EF-G) (NCBI ptt file) 188, 292
BC0129 BC0129 Protein Translation Elongation Factor Tu (EF-TU) (NCBI ptt file) 188, 430
BC0695 BC0695 Cytochrome aa3 quinol oxidase polypeptide IV (NCBI ptt file) 188, 380
BC0696 BC0696 Cytochrome aa3 quinol oxidase polypeptide III (NCBI ptt file) 14, 188
BC0697 BC0697 Cytochrome aa3 quinol oxidase polypeptide I (NCBI ptt file) 14, 188
BC0698 BC0698 Cytochrome aa3 quinol oxidase polypeptide II (NCBI ptt file) 14, 188
BC1482 BC1482 Riboflavin transporter (NCBI ptt file) 70, 166
BC1581 BC1581 Mg(2+) P-type ATPase-like protein (NCBI ptt file) 70, 505
BC1936 BC1936 Transcriptional regulator, MarR family (NCBI ptt file) 70, 129
BC1937 BC1937 Luciferase-like monooxygenase (NCBI ptt file) 70, 129
BC2358 BC2358 Cold shock protein (NCBI ptt file) 70, 350
BC3539 BC3539 Cold shock protein (NCBI ptt file) 70, 350
BC3970 BC3970 Dihydrolipoamide dehydrogenase (NCBI ptt file) 70, 188
BC3971 BC3971 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (NCBI ptt file) 70, 188
BC3972 BC3972 Pyruvate dehydrogenase E1 component beta subunit (NCBI ptt file) 70, 188
BC3973 BC3973 Pyruvate dehydrogenase E1 component alpha subunit (NCBI ptt file) 70, 188
BC4048 BC4048 Phosphoenolpyruvate-protein phosphotransferase (NCBI ptt file) 188, 471
BC4049 BC4049 Phosphocarrier protein HPr (NCBI ptt file) 70, 188
BC4050 BC4050 PTS system, glucose-specific IIABC component (NCBI ptt file) 188, 311
BC4859 BC4859 Cold shock protein (NCBI ptt file) 70, 350
BC5016 BC5016 60 kDa inner membrane protein YIDC (NCBI ptt file) 70, 129
BC5017 BC5017 hypothetical protein (NCBI ptt file) 70, 129
BC5135 BC5135 Enolase (NCBI ptt file) 28, 188
BC5136 BC5136 Phosphoglycerate mutase (NCBI ptt file) 70, 188
BC5137 BC5137 None 70, 188
BC5140 BC5140 Glyceraldehyde 3-phosphate dehydrogenase (NCBI ptt file) 70, 188
BC5141 BC5141 Central glycolytic genes regulator (NCBI ptt file) 70, 188
BC5189 BC5189 Protein translocase subunit SecA (NCBI ptt file) 70, 426
VIMSS12791523 VIMSS12791523 None 70, 188
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 BC5141
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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