Organism : Bacillus cereus ATCC14579 | Module List :
BC0616

Iron(III) dicitrate-binding protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog/ cog
iron ion transmembrane transporter activity go/ molecular_function
high-affinity iron ion transport go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0616
(Mouseover regulator name to see its description)

BC0616 is regulated by 24 influences and regulates 0 modules.
Regulators for BC0616 (24)
Regulator Module Operator
BC0405 7 tf
BC0630 7 tf
BC0806 7 tf
BC0961 7 tf
BC1932 7 tf
BC2122 7 tf
BC2558 7 tf
BC3163 7 tf
BC3244 7 tf
BC4256 7 tf
BC4826 7 tf
BC5171 7 tf
BC0224 443 tf
BC0266 443 tf
BC0435 443 tf
BC1282 443 tf
BC3704 443 tf
BC4174 443 tf
BC4256 443 tf
BC4499 443 tf
BC4826 443 tf
BC5205 443 tf
BC5339 443 tf
BC5434 443 tf

Warning: BC0616 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
3936 3.90e-03 TCccCTtcTttttcT
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3937 3.90e+03 ctCACTtTAT
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4796 4.70e+03 GcGAGCGC
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4797 1.10e+04 CTCACCGC
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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 BC0616

BC0616 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog/ cog
iron ion transmembrane transporter activity go/ molecular_function
high-affinity iron ion transport go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for BC0616

BC0616 has total of 59 gene neighbors in modules 7, 443
Gene neighbors (59)
Gene Common Name Description Module membership
BC0205 BC0205 hypothetical protein (NCBI ptt file) 7, 477
BC0224 BC0224 Transcriptional regulators, LysR family (NCBI ptt file) 221, 443
BC0435 BC0435 Transcriptional regulator, PBSX family (NCBI ptt file) 103, 443
BC0458 BC0458 Alkaline phosphatase like protein (NCBI ptt file) 354, 443
BC0459 BC0459 Bacterial/Archaeal Transporter family protein (NCBI ptt file) 304, 443
BC0517 BC0517 Thioredoxin-dependent thiol peroxidase (NCBI ptt file) 243, 443
BC0616 BC0616 Iron(III) dicitrate-binding protein (NCBI ptt file) 7, 443
BC0630 BC0630 Trehalose operon transcriptional repressor (NCBI ptt file) 7, 475
BC0681 BC0681 hypothetical protein (NCBI ptt file) 7, 294
BC0786 BC0786 Nitroreductase family (NCBI ptt file) 389, 443
BC0805 BC0805 outer surface protein (NCBI ptt file) 7, 380
BC0806 BC0806 Transcription antiterminator, BglG family (NCBI ptt file) 7, 290
BC0961 BC0961 Transcriptional regulator, TetR family (NCBI ptt file) 7, 401
BC0995 BC0995 hypothetical protein (NCBI ptt file) 343, 443
BC1133 BC1133 hypothetical protein (NCBI ptt file) 7, 354
BC1151 BC1151 IG hypothetical 17028 (NCBI ptt file) 414, 443
BC1177 BC1177 None 7, 74
BC1345 BC1345 hypothetical protein (NCBI ptt file) 7, 401
BC1349 BC1349 Acetyltransferase (NCBI ptt file) 7, 264
BC1601 BC1601 hypothetical protein (NCBI ptt file) 7, 146
BC1617 BC1617 hypothetical Cytosolic Protein (NCBI ptt file) 257, 443
BC1962 BC1962 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 7, 264
BC2045 BC2045 hypothetical protein (NCBI ptt file) 228, 443
BC2062 BC2062 hypothetical protein (NCBI ptt file) 7, 434
BC2516 BC2516 Short chain dehydrogenase (NCBI ptt file) 7, 220
BC2558 BC2558 Transcriptional regulator (NCBI ptt file) 7, 440
BC2585 BC2585 Portal protein (NCBI ptt file) 7, 316
BC2659 BC2659 Glutamate-rich protein grpB (NCBI ptt file) 7, 294
BC2690 BC2690 Quaternary ammonium compound-resistance protein (NCBI ptt file) 443, 468
BC2908 BC2908 hypothetical protein (NCBI ptt file) 7, 228
BC2950 BC2950 putative kinase (NCBI ptt file) 7, 364
BC2957 BC2957 hypothetical protein (NCBI ptt file) 7, 401
BC2995 BC2995 hypothetical protein (NCBI ptt file) 7, 100
BC2996 BC2996 Transcriptional regulator, PadR family (NCBI ptt file) 7, 440
BC3279 BC3279 hypothetical protein (NCBI ptt file) 7, 440
BC3318 BC3318 hypothetical protein (NCBI ptt file) 7, 100
BC3331 BC3331 hypothetical protein (NCBI ptt file) 7, 517
BC3333 BC3333 hypothetical Cytosolic Protein (NCBI ptt file) 7, 478
BC3411 BC3411 XoxI (NCBI ptt file) 7, 478
BC3448 BC3448 hypothetical Cytosolic Protein (NCBI ptt file) 7, 228
BC3536 BC3536 hypothetical protein (NCBI ptt file) 7, 517
BC3577 BC3577 Amino acid permease (NCBI ptt file) 389, 443
BC3606 BC3606 Esterase (NCBI ptt file) 7, 401
BC3704 BC3704 LexA repressor (NCBI ptt file) 414, 443
BC4108 BC4108 hypothetical protein (NCBI ptt file) 354, 443
BC4241 BC4241 hypothetical protein (NCBI ptt file) 7, 199
BC4337 BC4337 hypothetical Membrane Spanning Protein (NCBI ptt file) 440, 443
BC4345 BC4345 Lipase (NCBI ptt file) 221, 443
BC4532 BC4532 hypothetical protein (NCBI ptt file) 7, 440
BC4675 BC4675 Sex pheromone staph-cAM373 precursor (NCBI ptt file) 7, 100
BC4957 BC4957 hypothetical protein (NCBI ptt file) 343, 443
BC5170 BC5170 Integral membrane protein (NCBI ptt file) 7, 337
BC5171 BC5171 Transcriptional regulator, MerR family (NCBI ptt file) 7, 337
BC5187 BC5187 Cytochrome c551 (NCBI ptt file) 7, 481
BC5249 BC5249 hypothetical protein (NCBI ptt file) 354, 443
BC5381 BC5381 Ferrichrome transport ATP-binding protein fhuC (NCBI ptt file) 389, 443
BC5434 BC5434 Transcriptional regulator, TetR family (NCBI ptt file) 222, 443
BC5478 BC5478 hypothetical Cytosolic Protein (NCBI ptt file) 281, 443
BC5490 BC5490 LSU ribosomal protein L34P (NCBI ptt file) 7, 517
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 BC0616
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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