Organism : Bacillus subtilis | Module List :
BSU38770 cimH

citrate/malate/H+ symporter (RefSeq)

CircVis
Functional Annotations (5)
Function System
Na+/citrate symporter cog/ cog
organic anion transmembrane transporter activity go/ molecular_function
organic anion transport go/ biological_process
integral to membrane go/ cellular_component
ccs tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU38770
(Mouseover regulator name to see its description)

BSU38770 is regulated by 21 influences and regulates 0 modules.
Regulators for BSU38770 cimH (21)
Regulator Module Operator
BSU00470 329 tf
BSU02220 329 tf
BSU06960 329 tf
BSU08990 329 tf
BSU10860 329 tf
BSU13340 329 tf
BSU16170 329 tf
BSU19030 329 tf
BSU33950 329 tf
BSU35520 329 tf
BSU00470 359 tf
BSU00800 359 tf
BSU08990 359 tf
BSU09380 359 tf
BSU10860 359 tf
BSU15970 359 tf
BSU16600 359 tf
BSU19090 359 tf
BSU33080 359 tf
BSU35050 359 tf
BSU36020 359 tf

Warning: BSU38770 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
5596 1.90e-05 Aa.GAAAgCGCTtaa
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5597 7.50e+02 tGGcAcg.tcCTTgcatt
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5642 3.80e-06 AaAGGaGGaa
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5643 3.10e+04 CCGCCCaACTC
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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 BSU38770

BSU38770 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Na+/citrate symporter cog/ cog
organic anion transmembrane transporter activity go/ molecular_function
organic anion transport go/ biological_process
integral to membrane go/ cellular_component
ccs tigr/ tigrfam
Module neighborhood information for BSU38770

BSU38770 has total of 50 gene neighbors in modules 329, 359
Gene neighbors (50)
Gene Common Name Description Module membership
BSU01560 kbaA inner membrane protein involved in activation of the KinB signaling pathway to sporulation (RefSeq) 31, 359
BSU02310 ybfO putative exported hydrolase (RefSeq) 306, 329
BSU03630 yclB aromatic acid decarboxylase (RefSeq) 208, 329
BSU03640 ubiD putative 3-polyprenyl-4-hydroxybenzoate decarboxylase (RefSeq) 329, 350
BSU06140 gutR transcriptional regulator of the glucitol operon (RefSeq) 26, 359
BSU06230 iolT myo-inositol transporter (RefSeq) 329, 407
BSU07450 yfmJ putative oxidoreductase (RefSeq) 90, 359
BSU07530 yfmB hypothetical protein (RefSeq) 222, 359
BSU07540 yfmA hypothetical protein (RefSeq) 222, 359
BSU12360 exuT hexuronate transporter (RefSeq) 33, 329
BSU13340 ykoM putative transcriptional regulator (MarR family) (RefSeq) 329, 330
BSU13990 kinA sporulation-specific ATP-dependent protein histidine kinase (RefSeq) 205, 359
BSU14220 ykuU putative 2-cys peroxiredoxin (RefSeq) 91, 359
BSU14230 ykuV thiol-disulfide isomerase (RefSeq) 91, 359
BSU17240 ymzB hypothetical protein (RefSeq) 165, 359
BSU17250 ymaE putative hydrolase (RefSeq) 114, 359
BSU17340 hfq RNA-binding protein Hfq (RefSeq) 95, 359
BSU19400 sodC superoxide dismutase (exported lipoprotein) (RefSeq) 239, 359
BSU26820 yrpD putative lipoprotein (RefSeq) 25, 359
BSU27030 sacC levanase (RefSeq) 85, 329
BSU27070 levD phosphotransferase system (PTS) fructose-specific enzyme IIA component (RefSeq) 85, 329
BSU28700 ysfE hypothetical protein (RefSeq) 329, 330
BSU28810 abnA arabinan-endo 1,5-alpha-L-arabinase (RefSeq) 22, 329
BSU29540 ppnK inorganic polyphosphate/ATP-NAD kinase (RefSeq) 77, 359
BSU31000 yuaI putative acetyl-transferase (RefSeq) 329, 407
BSU31540 yufN putative lipoprotein (RefSeq) 329, 350
BSU31720 degQ pleiotropic regulator (RefSeq) 61, 329
BSU32990 mrgA metalloregulation DNA-binding stress protein (RefSeq) 296, 359
BSU33240 oxdC oxalate decarboxylase (RefSeq) 329, 407
BSU33960 araE arabinose-related compounds permease (RefSeq) 91, 329
BSU34390 pnbA para-nitrobenzyl esterase (intracellular esterase B) (RefSeq) 353, 359
BSU34430 racX amino acid racemase (RefSeq) 91, 329
BSU34440 pbpE penicillin-binding protein 4* (RefSeq) 91, 329
BSU37220 ywjB putative oxidoreductase (RefSeq) 359, 391
BSU37230 ywjA putative ABC lipid transporter (ATP-binding protein) (RefSeq) 359, 391
BSU37760 rocC arginine/ornithine permease (RefSeq) 329, 407
BSU37770 rocB putative N-deacylase involved in arginine and ornithine utilization (RefSeq) 329, 407
BSU37780 rocA 1-pyrroline-5-carboxylate dehydrogenase (RefSeq) 329, 407
BSU37790 rocG glutamate dehydrogenase (RefSeq) 329, 407
BSU38040 sacA sucrase-6-phosphate hydrolase (RefSeq) 248, 359
BSU38050 sacP phosphotransferase system (PTS) sucrose-specific enzyme IIBC component (RefSeq) 329, 330
BSU38770 cimH citrate/malate/H+ symporter (RefSeq) 329, 359
BSU39070 bglS endo-beta-1,3-1,4 glucanase (RefSeq) 61, 329
BSU39100 yxiO putative efflux transporter (RefSeq) 215, 359
BSU39870 yxbD putative acetyltransferase (RefSeq) 25, 359
BSU40180 yydF peptide controlling LiaRS (RefSeq) 114, 359
BSU40460 yyzB hypothetical protein (RefSeq) 359, 387
BSU40820 yyaL hypothetical protein (RefSeq) 81, 359
VIMSS36712 VIMSS36712 None 45, 329
VIMSS37376 VIMSS37376 None 235, 329
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 BSU38770
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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