Organism : Clostridium acetobutylicum | Module List :
CAC2949

Predicted permease (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted permeases cog/ cog
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2949
(Mouseover regulator name to see its description)

CAC2949 is regulated by 14 influences and regulates 0 modules.
Regulators for CAC2949 (14)
Regulator Module Operator
CAC0093 309 tf
CAC0550 309 tf
CAC0723 309 tf
CAC1333 309 tf
CAC1766 309 tf
CAC3433 309 tf
CAC3438 309 tf
CAC3487 309 tf
CAC3651 309 tf
CAC0093 207 tf
CAC0144 207 tf
CAC0197 207 tf
CAC3466 207 tf
CAC3509 207 tf

Warning: CAC2949 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
7066 4.30e-11 gAGGtGat
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7067 7.10e+02 AGcaGtggCc
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7270 1.50e-04 CACAgaTtTcTtTAttTgTagcAc
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7271 4.90e-03 GTGAcaCAcaTGTGctaCacGA
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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 CAC2949

CAC2949 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted permeases cog/ cog
integral to membrane go/ cellular_component
Module neighborhood information for CAC2949

CAC2949 has total of 47 gene neighbors in modules 207, 309
Gene neighbors (47)
Gene Common Name Description Module membership
CAC0079 CAC0079 Hypothetical protein (NCBI ptt file) 219, 309
CAC0168 CAC0168 T-RNA-processing ribonuclease BN (NCBI ptt file) 82, 207
CAC0204 srta Sortase (surface protein transpeptidase), YHCS B.subtilis ortholog (NCBI ptt file) 115, 207
CAC0222 exoA Exodeoxyribonuclease (exoA) (NCBI ptt file) 72, 207
CAC0250 CAC0250 Methyl-accepting chemotaxis protein (NCBI ptt file) 207, 258
CAC0314 CAC0314 Uncharacterized protein homolog YKRK B. subtilis (NCBI ptt file) 57, 207
CAC0345 CAC0345 Hypothetical protein (NCBI ptt file) 207, 361
CAC0347 CAC0347 Hypothetical protein (NCBI ptt file) 309, 344
CAC0351 CAC0351 Hypothetical protein (NCBI ptt file) 89, 309
CAC0357 CAC0357 Permease of the Na:galactoside symporter family (NCBI ptt file) 207, 361
CAC0358 CAC0358 Predicted xylanase/chitin deacetylase (NCBI ptt file) 165, 207
CAC0431 CAC0431 Hypothetical protein, YitT family (NCBI ptt file) 169, 207
CAC0440 CAC0440 Homolog of osmotically induced OSMY protein of E.coli (NCBI ptt file) 62, 207
CAC0463 CAC0463 Serine protease Do (heat-shock protein) (NCBI ptt file) 207, 223
CAC0543 CAC0543 Methyl-accepting chemotaxis protein (NCBI ptt file) 207, 361
CAC0607 CAC0607 Aspartyl aminopeptidase (NCBI ptt file) 287, 309
CAC0628 CAC0628 Putative Mn transporter, NRAMR family (NCBI ptt file) 191, 207
CAC0722 CAC0722 Predicted membrane protein; CF-9 family (NCBI ptt file) 4, 309
CAC0723 CAC0723 Transcriptional regulator, AcrR family (NCBI ptt file) 157, 309
CAC0724 CAC0724 Transcriptional regulator, AcrR family (NCBI ptt file) 132, 309
CAC0725 CAC0725 Predicted membrane protein; CF-9 family (NCBI ptt file) 132, 309
CAC0755 CAC0755 Multimeric flavodoxin WrbA family protein, diverged or disrupted (NCBI ptt file) 89, 309
CAC0756 CAC0756 Multimeric flavodoxin WrbA (NCBI ptt file) 157, 309
CAC0805 CAC0805 Methyl-accepting chemotaxis protein (NCBI ptt file) 24, 207
CAC0833 CAC0833 ABC-type multidrug transport system (daunorubicin resistance), ATPase component (NCBI ptt file) 115, 207
CAC0835 CAC0835 Predicted integral membrane protein (NCBI ptt file) 115, 207
CAC0886 CAC0886 Hypothetical protein (NCBI ptt file) 207, 270
CAC1011 CAC1011 Uncharacterized small membrane protein, homolog of ykvA B.subtilis (NCBI ptt file) 282, 309
CAC1186 CAC1186 Hypothetical protein (NCBI ptt file) 89, 309
CAC1422 CAC1422 Uncharacterized CBS domain-containing protein, YUGS B.subtilis ortholog (NCBI ptt file) 207, 361
CAC1827 CAC1827 TldD-like protein fragment (NCBI ptt file) 74, 309
CAC2057 CAC2057 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 102, 207
CAC2540 CAC2540 Co/Zn/Cd efflux system component (NCBI ptt file) 207, 301
CAC2664 CAC2664 Predicted phosphoesterase, YSNB B.subtilis ortholog (NCBI ptt file) 302, 309
CAC2765 CAC2765 Similar to uncharacterized domain of sensory transducer protein (NCBI ptt file) 176, 309
CAC2814 CAC2814 Predicted membrane protein (NCBI ptt file) 153, 207
CAC2949 CAC2949 Predicted permease (NCBI ptt file) 207, 309
CAC3024 CAC3024 acyl-CoA thioesterase family protein (NCBI ptt file) 216, 309
CAC3025 CAC3025 Conserved membrane protein, possible permease, YHCI B.subtilis ortholog (NCBI ptt file) 157, 309
CAC3347 CAC3347 Amino acid transporter, permease (NCBI ptt file) 207, 276
CAC3363 CAC3363 Hypothetical protein (NCBI ptt file) 89, 309
CAC3438 CAC3438 Transcriptional regulator, (BlaI/MecI subfamily) (NCBI ptt file) 89, 309
CAC3468 uvrC Excinuclease ABC, subunit C (uvrC) (NCBI ptt file) 207, 301
CAC3478 CAC3478 Predicted membrane protein (NCBI ptt file) 207, 326
CAC3487 CAC3487 Predicted transcriptional regulator (NCBI ptt file) 132, 309
CAC3519 CAC3519 Predicted membrane protein, possible permease (NCBI ptt file) 158, 207
CAC3520 CAC3520 ABC-type transport system, ATPase component (NCBI ptt file) 158, 207
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 CAC2949
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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