Organism : Clostridium acetobutylicum | Module List :
CAC0440

Homolog of osmotically induced OSMY protein of E.coli (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted periplasmic or secreted lipoprotein cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0440
(Mouseover regulator name to see its description)

CAC0440 is regulated by 18 influences and regulates 0 modules.
Regulators for CAC0440 (18)
Regulator Module Operator
CAC0093 207 tf
CAC0144 207 tf
CAC0197 207 tf
CAC3466 207 tf
CAC3509 207 tf
CAC0023 62 tf
CAC0195 62 tf
CAC0859 62 tf
CAC0863 62 tf
CAC1430 62 tf
CAC1536 62 tf
CAC1578 62 tf
CAC2254 62 tf
CAC2934 62 tf
CAC3166 62 tf
CAC3418 62 tf
CAC3466 62 tf
CAC3504 62 tf

Warning: CAC0440 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
6778 4.90e-04 GgAGGt
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6779 3.30e+02 GGagaagG
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7066 4.30e-11 gAGGtGat
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7067 7.10e+02 AGcaGtggCc
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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 CAC0440

CAC0440 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted periplasmic or secreted lipoprotein cog/ cog
Module neighborhood information for CAC0440

CAC0440 has total of 52 gene neighbors in modules 62, 207
Gene neighbors (52)
Gene Common Name Description Module membership
CAC0009 CAC0009 Uncharacterized conserved protein, ortholog of YRXA B.subtilis (NCBI ptt file) 62, 312
CAC0134 CAC0134 Hypothetical protein, CF-19 family (NCBI ptt file) 62, 247
CAC0146 CAC0146 Related to ABC transporter permease component (NCBI ptt file) 62, 142
CAC0147 CAC0147 ABC transporter, ATP-binding protein (NCBI ptt file) 62, 142
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
CAC0205 CAC0205 Predicted phosphohydrolases, Icc family (NCBI ptt file) 62, 279
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
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
CAC0444 napA Na/H antiporter (napA) (NCBI ptt file) 62, 174
CAC0463 CAC0463 Serine protease Do (heat-shock protein) (NCBI ptt file) 207, 223
CAC0543 CAC0543 Methyl-accepting chemotaxis protein (NCBI ptt file) 207, 361
CAC0628 CAC0628 Putative Mn transporter, NRAMR family (NCBI ptt file) 191, 207
CAC0738 CAC0738 DNA polymerase III epsilon subunit (3'-5' exonuclease) containing BRCT domain (NCBI ptt file) 62, 142
CAC0750 CAC0750 Hypothetical protein (NCBI ptt file) 62, 342
CAC0779 CAC0779 Amidase related to nicotinamidase (NCBI ptt file) 39, 62
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
CAC0934 CAC0934 Hypothetical protein (NCBI ptt file) 62, 177
CAC1019 CAC1019 Phospholipase C related protein (NCBI ptt file) 62, 80
CAC1238 CAC1238 Hypothetical protein (NCBI ptt file) 62, 348
CAC1422 CAC1422 Uncharacterized CBS domain-containing protein, YUGS B.subtilis ortholog (NCBI ptt file) 207, 361
CAC1860 CAC1860 Predicted flavodoxin oxidoreductase (NCBI ptt file) 62, 312
CAC2057 CAC2057 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 102, 207
CAC2431 CAC2431 Alkaline phosphatase superfamily enzyme (NCBI ptt file) 62, 312
CAC2540 CAC2540 Co/Zn/Cd efflux system component (NCBI ptt file) 207, 301
CAC2682 CAC2682 Hypothetical protein (NCBI ptt file) 62, 300
CAC2683 cotF Related to spore coat protein F (NCBI ptt file) 62, 300
CAC2776 CAC2776 Hypothetical protein (NCBI ptt file) 62, 102
CAC2781 CAC2781 Hypothetical protein (NCBI ptt file) 62, 345
CAC2814 CAC2814 Predicted membrane protein (NCBI ptt file) 153, 207
CAC2938 CAC2938 Hypothetical protein (NCBI ptt file) 5, 62
CAC2949 CAC2949 Predicted permease (NCBI ptt file) 207, 309
CAC3168 CAC3168 Predicted membrane protein (NCBI ptt file) 62, 344
CAC3232 CAC3232 Hypothetical protein (NCBI ptt file) 62, 247
CAC3347 CAC3347 Amino acid transporter, permease (NCBI ptt file) 207, 276
CAC3379 CAC3379 Uncharacterized protein, YQFW B.subtilis homolog (NCBI ptt file) 62, 361
CAC3392 CAC3392 NADH-dependent butanol dehydrogenase (NCBI ptt file) 62, 91
CAC3468 uvrC Excinuclease ABC, subunit C (uvrC) (NCBI ptt file) 207, 301
CAC3478 CAC3478 Predicted membrane protein (NCBI ptt file) 207, 326
CAC3504 CAC3504 Transcriptional regulator, AcrR family (NCBI ptt file) 62, 235
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
CAC3601 CAC3601 Nudix (MutT) family hydrolase (NCBI ptt file) 62, 259
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 CAC0440
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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