Organism : Bacillus cereus ATCC14579 | Module List :
BC2888

Integral membrane protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2888
(Mouseover regulator name to see its description)

BC2888 is regulated by 18 influences and regulates 0 modules.
Regulators for BC2888 (18)
Regulator Module Operator
BC0648 489 tf
BC1059 489 tf
BC1489 489 tf
BC1531 489 tf
BC2903 489 tf
BC3449 489 tf
BC3702 489 tf
BC3961 489 tf
BC4029 489 tf
BC4336 489 tf
BC4832 489 tf
BC1710 153 tf
BC2410 153 tf
BC2469 153 tf
BC3039 153 tf
BC3587 153 tf
BC3904 153 tf
BC5251 153 tf

Warning: BC2888 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
4222 9.50e-04 AAatag.aaaGggGagATt.t
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4223 2.70e+00 cCtCC.cATcTcTTAT
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4888 8.80e-02 AaGGAGag
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4889 4.20e+04 T.tATcA.TTcTTt.TGttgt
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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 BC2888

BC2888 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
integral to membrane go/ cellular_component
Module neighborhood information for BC2888

BC2888 has total of 42 gene neighbors in modules 153, 489
Gene neighbors (42)
Gene Common Name Description Module membership
BC0559 BC0559 Methyl-accepting chemotaxis protein (NCBI ptt file) 489, 517
BC0560 BC0560 Two component system histidine kinase (NCBI ptt file) 489, 516
BC0605 BC0605 hypothetical protein (NCBI ptt file) 155, 489
BC0860 BC0860 Multidrug resistance protein B (NCBI ptt file) 144, 489
BC0983 BC0983 hypothetical protein (NCBI ptt file) 153, 454
BC1046 BC1046 hypothetical protein (NCBI ptt file) 9, 489
BC1124 BC1124 Methyl-accepting chemotaxis protein (NCBI ptt file) 428, 489
BC1278 BC1278 Signal peptidase I (NCBI ptt file) 155, 489
BC1561 BC1561 hypothetical Cytosolic Protein (NCBI ptt file) 10, 489
BC1600 BC1600 Ribonuclease H (NCBI ptt file) 454, 489
BC2016 BC2016 Amine oxidase [flavin-containing] (NCBI ptt file) 153, 168
BC2227 BC2227 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 104, 153
BC2228 BC2228 hypothetical protein (NCBI ptt file) 61, 153
BC2318 BC2318 hypothetical protein (NCBI ptt file) 97, 489
BC2334 BC2334 hypothetical Membrane Spanning Protein (NCBI ptt file) 115, 153
BC2335 BC2335 Catabolite gene activator (NCBI ptt file) 153, 411
BC2594 BC2594 Phage protein (NCBI ptt file) 111, 153
BC2595 BC2595 Gp13 protein (NCBI ptt file) 153, 376
BC2596 BC2596 Phage endopeptidase (NCBI ptt file) 153, 446
BC2597 BC2597 Phage protein (NCBI ptt file) 111, 153
BC2601 BC2601 hypothetical protein (NCBI ptt file) 147, 489
BC2607 BC2607 hypothetical protein (NCBI ptt file) 308, 489
BC2696 BC2696 Intein-containing protein (NCBI ptt file) 84, 489
BC2746 BC2746 hypothetical protein (NCBI ptt file) 435, 489
BC2819 BC2819 hypothetical protein (NCBI ptt file) 85, 489
BC2847 BC2847 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 404, 489
BC2888 BC2888 Integral membrane protein (NCBI ptt file) 153, 489
BC3038 BC3038 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 96, 153
BC3039 BC3039 Transcriptional regulator, GntR family (NCBI ptt file) 153, 250
BC3214 BC3214 hypothetical protein (NCBI ptt file) 30, 489
BC3319 BC3319 hypothetical protein (NCBI ptt file) 289, 489
BC3408 BC3408 Transcriptional regulator, MarR family (NCBI ptt file) 454, 489
BC3449 BC3449 Catabolite gene activator (NCBI ptt file) 454, 489
BC3564 BC3564 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 153, 267
BC3565 BC3565 Molybdopterin (MPT) converting factor, subunit 2 (NCBI ptt file) 153, 398
BC3716 BC3716 None 153, 376
BC3961 BC3961 putative transcriptional regulator (NCBI ptt file) 364, 489
BC4513 BC4513 Chemotaxis motA protein (NCBI ptt file) 248, 489
BC4611 BC4611 Cytosolic protein containing multiple CBS domains (NCBI ptt file) 97, 489
BC4816 BC4816 hypothetical protein (NCBI ptt file) 276, 489
BC5114 BC5114 hypothetical protein (NCBI ptt file) 489, 498
BC5234 BC5234 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 276, 489
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 BC2888
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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