Organism : Bacillus cereus ATCC14579 | Module List :
BC3503

Transporter, Sodium/bile acid symporter family (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3503
(Mouseover regulator name to see its description)

BC3503 is regulated by 30 influences and regulates 0 modules.
Regulators for BC3503 (30)
Regulator Module Operator
BC0224 120 tf
BC0356 120 tf
BC0473 120 tf
BC0648 120 tf
BC1936 120 tf
BC2217 120 tf
BC3207 120 tf
BC3244 120 tf
BC3493 120 tf
BC3653 120 tf
BC3844 120 tf
BC4104 120 tf
BC4525 120 tf
BC4652 120 tf
BC4930 120 tf
BC0598 194 tf
BC0613 194 tf
BC0648 194 tf
BC2770 194 tf
BC3072 194 tf
BC3095 194 tf
BC3405 194 tf
BC3653 194 tf
BC3826 194 tf
BC3844 194 tf
BC3922 194 tf
BC4072 194 tf
BC4499 194 tf
BC4525 194 tf
BC4652 194 tf

Warning: BC3503 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
4156 1.50e-01 aAgAGGaG
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4157 1.60e+01 AaAtacagaAAATtCctTcTa
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4304 2.80e+00 AGGgGg
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4305 2.40e+03 AAaGAGGTG
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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 BC3503

Warning: No Functional annotations were found!

Module neighborhood information for BC3503

BC3503 has total of 47 gene neighbors in modules 120, 194
Gene neighbors (47)
Gene Common Name Description Module membership
BC0168 BC0168 Mrp protein (NCBI ptt file) 194, 475
BC0707 BC0707 Ferrous iron transport protein B (NCBI ptt file) 194, 335
BC0708 BC0708 Ferrous iron transport protein B (NCBI ptt file) 194, 335
BC0709 BC0709 Ferrous iron transport protein A (NCBI ptt file) 194, 335
BC0864 BC0864 Protein ecsB (NCBI ptt file) 194, 491
BC0867 BC0867 hypothetical protein (NCBI ptt file) 194, 359
BC0901 BC0901 Deblocking aminopeptidase (NCBI ptt file) 47, 194
BC1071 BC1071 hypothetical protein (NCBI ptt file) 194, 330
BC1226 BC1226 Acetyl esterase (NCBI ptt file) 194, 328
BC1270 BC1270 hypothetical protein (NCBI ptt file) 120, 488
BC1312 BC1312 3-hydroxybutyryl-CoA dehydratase (NCBI ptt file) 73, 120
BC1313 BC1313 PhaP protein (NCBI ptt file) 73, 120
BC1314 BC1314 PhaQ protein (NCBI ptt file) 73, 120
BC1315 BC1315 PhaQ protein (NCBI ptt file) 73, 120
BC1316 BC1316 PhaR protein (NCBI ptt file) 73, 120
BC1317 BC1317 Acetoacetyl-CoA reductase (NCBI ptt file) 73, 120
BC1318 BC1318 Poly-beta-hydroxybutyrate polymerase (NCBI ptt file) 73, 120
BC1726 BC1726 hypothetical Membrane Spanning Protein (NCBI ptt file) 47, 194
BC1783 BC1783 Capsule biosynthesis protein capA (NCBI ptt file) 120, 264
BC1828 BC1828 Xaa-Pro aminopeptidase (NCBI ptt file) 194, 258
BC1992 BC1992 hypothetical protein (NCBI ptt file) 120, 488
BC1993 BC1993 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 120, 488
BC2024 BC2024 O6-methylguanine-DNA methyltransferase (NCBI ptt file) 194, 302
BC2025 BC2025 hypothetical protein (NCBI ptt file) 72, 194
BC2055 BC2055 Macrolide-efflux protein (NCBI ptt file) 194, 414
BC2064 BC2064 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 120, 381
BC2065 BC2065 hypothetical protein (NCBI ptt file) 120, 381
BC2197 BC2197 Sec-independent protein translocase protein tatA (NCBI ptt file) 120, 258
BC2198 BC2198 Sec-independent protein translocase protein tatC (NCBI ptt file) 120, 488
BC2209 BC2209 D-amino acid aminotransferase (RefSeq) 120, 284
BC2230 BC2230 Macrolide-efflux protein (NCBI ptt file) 194, 208
BC2436 BC2436 SpoIISA like protein (NCBI ptt file) 194, 322
BC3503 BC3503 Transporter, Sodium/bile acid symporter family (NCBI ptt file) 120, 194
BC3623 BC3623 hypothetical protein (NCBI ptt file) 120, 488
BC3711 BC3711 DNA integration/recombination/invertion protein (NCBI ptt file) 194, 414
BC3938 BC3938 hypothetical Cytosolic Protein (NCBI ptt file) 120, 264
BC4003 BC4003 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI ptt file) 194, 218
BC4023 BC4023 Acetyl-CoA acetyltransferase (NCBI ptt file) 112, 120
BC4063 BC4063 hydrolase (HAD superfamily) (NCBI ptt file) 120, 264
BC4104 BC4104 Ribose operon repressor (NCBI ptt file) 120, 488
BC4133 BC4133 Zinc metallohydrolase (NCBI ptt file) 137, 194
BC4257 BC4257 hypothetical Cytosolic Protein (NCBI ptt file) 194, 225
BC4623 BC4623 Alanine dehydrogenase (NCBI ptt file) 48, 194
BC4634 BC4634 Protein ecsC (NCBI ptt file) 194, 438
BC4642 BC4642 ATP-NAD kinase (NCBI ptt file) 120, 488
BC5091 BC5091 SnoK-like protein (NCBI ptt file) 73, 120
BC5092 BC5092 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (NCBI ptt file) 73, 120
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 BC3503
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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