Organism : Clostridium acetobutylicum | Module List :
CAC1950

Hypothetical protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulator cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1950
(Mouseover regulator name to see its description)

CAC1950 is regulated by 16 influences and regulates 10 modules.
Regulators for CAC1950 (16)
Regulator Module Operator
CAC0859 117 tf
CAC1340 117 tf
CAC1578 117 tf
CAC1950 117 tf
CAC2608 117 tf
CAC3152 117 tf
CAC3507 117 tf
CAC3611 117 tf
CAC1264 345 tf
CAC1696 345 tf
CAC1950 345 tf
CAC2055 345 tf
CAC2608 345 tf
CAC2773 345 tf
CAC3424 345 tf
CAC3611 345 tf

Warning: CAC1950 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
6886 1.10e+02 gCtTCggcTt
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6887 1.40e+00 AGGaGg
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7342 1.60e-09 aAGGgGGA
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7343 7.90e+03 GCTTcGGC
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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 CAC1950

CAC1950 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulator cog/ cog
Module neighborhood information for CAC1950

CAC1950 has total of 49 gene neighbors in modules 117, 345
Gene neighbors (49)
Gene Common Name Description Module membership
CAC0148 CAC0148 Predicted enzyme with TIM-barrel fold (NCBI ptt file) 117, 345
CAC0160 CAC0160 Predicted acetyltransferase (NCBI ptt file) 185, 345
CAC0177 appB Oligopeptide transport permease protein (NCBI ptt file) 314, 345
CAC0248 CAC0248 Transposon related protein (NCBI ptt file) 13, 117
CAC0325 CAC0325 Uncharacterized membrane protein, homolog of YtaF B.subtilis (NCBI ptt file) 13, 117
CAC0352 CAC0352 Uncharacterized conserved membrane protein, SANA family (NCBI ptt file) 115, 345
CAC0583 CAC0583 CBIK protein (chain A, anaerobic cobalt chelatase) (NCBI ptt file) 117, 344
CAC0584 CAC0584 Precorrin-6B methylase 1 CobL1/CbiE (NCBI ptt file) 106, 117
CAC0746 CAC0746 Secreted protease metal-dependent protease (NCBI ptt file) 269, 345
CAC0994 CAC0994 Predicted membrane protein (NCBI ptt file) 100, 345
CAC0995 CAC0995 Predicted membrane protein (NCBI ptt file) 80, 345
CAC1049 CAC1049 Uncharacterized conserved protein,ortholog of YaaR B.subtilis (NCBI ptt file) 117, 158
CAC1160 CAC1160 Hypothetical protein (NCBI ptt file) 25, 345
CAC1266 CAC1266 Pseudouridylate synthase family protein, yabo B.subtilis ortholog (NCBI ptt file) 67, 345
CAC1317 CAC1317 Potassium channel subunit (NCBI ptt file) 117, 344
CAC1450 CAC1450 Predicted alpha/beta superfamily hydrolase (NCBI ptt file) 294, 345
CAC1528 CAC1528 Predicted membrane protein (NCBI ptt file) 117, 336
CAC1543 CAC1543 Lactate dehydrogenase (NCBI ptt file) 117, 265
CAC1592 CAC1592 Predicted permease, YCGR B.subtilis ortholog (NCBI ptt file) 69, 345
CAC1614 CAC1614 Predicted glycosyltransferase (NCBI ptt file) 69, 117
CAC1791 CAC1791 Undecaprenyl pyrophosphate synthase (NCBI ptt file) 282, 345
CAC1911 CAC1911 Hypothetical protein (NCBI ptt file) 117, 345
CAC1921 CAC1921 Hypothetical protein (NCBI ptt file) 54, 117
CAC1922 CAC1922 Hypothetical protein (NCBI ptt file) 117, 246
CAC1948 CAC1948 Hypothetical protein (NCBI ptt file) 117, 261
CAC1949 CAC1949 Possible TPR-repeat contaning protein (NCBI ptt file) 117, 261
CAC1950 CAC1950 Hypothetical protein (NCBI ptt file) 117, 345
CAC2055 CAC2055 Predicted transcriptional regulator (NCBI ptt file) 158, 345
CAC2168 CAC2168 Uncharacterized conserved protein (NCBI ptt file) 258, 345
CAC2287 CAC2287 Acyl-CoA reductase LuxC (NCBI ptt file) 73, 345
CAC2298 CAC2298 Predicted nucleotidyltransferase (NCBI ptt file) 91, 345
CAC2301 mrcB Membrane carboxypeptidase mrcB (NCBI ptt file) 239, 345
CAC2343 CAC2343 LPS biosynthesis O-acetyl transferase (NCBI ptt file) 100, 345
CAC2414 CAC2414 Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file) 283, 345
CAC2418 CAC2418 Uncharacterized conserved membrane protein (NCBI ptt file) 117, 158
CAC2608 CAC2608 Trancriptional regulator of AraC family (NCBI ptt file) 117, 158
CAC2660 pykA Pyruvate carboxylase, PYKA (NCBI ptt file) 29, 345
CAC2687 recQ RecQ protein, superfamily II DNA helicase (NCBI ptt file) 113, 345
CAC2694 CAC2694 Hypothetical protein (NCBI ptt file) 158, 345
CAC2696 CAC2696 Predicted membrane protein (NCBI ptt file) 117, 346
CAC2781 CAC2781 Hypothetical protein (NCBI ptt file) 62, 345
CAC2907 CAC2907 Glycosyltransferase (NCBI ptt file) 13, 117
CAC2946 CAC2946 Hypothetical protein (NCBI ptt file) 345, 363
CAC2961 galT Galactose-1-phosphate uridyltransferase (NCBI ptt file) 75, 345
CAC2988 CAC2988 Uncharacterized conserved protein, YABE B.subtilis ortholog (NCBI ptt file) 267, 345
CAC3228 CAC3228 Predicted membrane protein (NCBI ptt file) 5, 117
CAC3424 CAC3424 Transcriptional regulator, RpiR family (NCBI ptt file) 158, 345
CAC3611 CAC3611 Regulatory protein related to malT, positive regulator of mal regulon (ATPase and HTH-type DNA-binding domain) (NCBI ptt file) 117, 158
CAC3683 CAC3683 Penicillin-binding protein 2 (serine-type D-Ala-D-Ala carboxypeptidase) (NCBI ptt file) 117, 286
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 CAC1950
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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