Organism : Clostridium acetobutylicum | Module List :
CAC2018

Aldehyde:ferredoxin oxidoreductase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Aldehyde:ferredoxin oxidoreductase cog/ cog
electron transport go/ biological_process
aldehyde ferredoxin oxidoreductase activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
regulation of cell cycle go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2018
(Mouseover regulator name to see its description)

CAC2018 is regulated by 24 influences and regulates 0 modules.
Regulators for CAC2018 (24)
Regulator Module Operator
CAC0255 209 tf
CAC0745 209 tf
CAC0821 209 tf
CAC1300 209 tf
CAC1426 209 tf
CAC1668 209 tf
CAC1766 209 tf
CAC2052 209 tf
CAC2394 209 tf
CAC2552 209 tf
CAC2842 209 tf
CAC3037 209 tf
CAC3063 209 tf
CAC3324 209 tf
CAC1226 134 tf
CAC1668 134 tf
CAC1698 134 tf
CAC1928 134 tf
CAC2071 134 tf
CAC2306 134 tf
CAC3360 134 tf
CAC3443 134 tf
CAC3646 134 tf
CAC3649 134 tf

Warning: CAC2018 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
6920 7.90e-09 tCACcccC
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6921 1.50e+03 cAGGTTCGcC
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7070 7.00e+01 CAacaGGcGg
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7071 7.60e+03 CGGtCc
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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 CAC2018

CAC2018 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Aldehyde:ferredoxin oxidoreductase cog/ cog
electron transport go/ biological_process
aldehyde ferredoxin oxidoreductase activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
regulation of cell cycle go/ biological_process
Module neighborhood information for CAC2018

CAC2018 has total of 41 gene neighbors in modules 134, 209
Gene neighbors (41)
Gene Common Name Description Module membership
CAC0555 CAC0555 Predicted membrane protein (NCBI ptt file) 7, 134
CAC0815 CAC0815 Methyl-accepting chemotaxis protein (NCBI ptt file) 134, 209
CAC0816 CAC0816 Lipase-esterase related protein (NCBI ptt file) 176, 209
CAC0869 CAC0869 Thioredoxine reductase (NCBI ptt file) 31, 209
CAC0902 CAC0902 Predicted membrane protein (NCBI ptt file) 134, 277
CAC0903 CAC0903 Sensory transduction histidine kinase (NCBI ptt file) 134, 277
CAC0982 CAC0982 Hypothetical protein (NCBI ptt file) 209, 266
CAC0987 CAC0987 Hypothetical protein (NCBI ptt file) 38, 134
CAC0988 CAC0988 Probably membrane protein (NCBI ptt file) 5, 134
CAC1103 CAC1103 Possible metal-binding domain, related to a correspondent domain of site-specific recombinase (NCBI ptt file) 134, 268
CAC1121 CAC1121 Predicted membrane protein (NCBI ptt file) 134, 152
CAC1169 CAC1169 Hypothetical protein (NCBI ptt file) 53, 134
CAC1480 CAC1480 Predicted dehydrogenase (NCBI ptt file) 113, 134
CAC1568 CAC1568 Diguanylate cyclase/phosphodiesterase domain 1 (GGDEF) (NCBI ptt file) 134, 162
CAC1587 CAC1587 Integral membrane protein possibly involved in chromosome condensation (NCBI ptt file) 134, 182
CAC1669 CstA Carbon starvation protein (NCBI ptt file) 209, 238
CAC1764 CAC1764 Predicted glutamine amidotransferase (NCBI ptt file) 31, 209
CAC1854 CAC1854 Nudix (MutT) family hydrolase (NCBI ptt file) 209, 277
CAC2004 CAC2004 Siderophore/Surfactin synthetase related protein (NCBI ptt file) 60, 209
CAC2007 CAC2007 Predicted glycosyltransferase (NCBI ptt file) 97, 209
CAC2011 fabH Possible 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file) 97, 209
CAC2016 fadB Enoyl-CoA hydratase (NCBI ptt file) 97, 209
CAC2017 CAC2017 Acyl carrier protein (NCBI ptt file) 134, 209
CAC2018 CAC2018 Aldehyde:ferredoxin oxidoreductase (NCBI ptt file) 134, 209
CAC2021 moeA Molybdopterin biosynthesis enzyme, MoeA (short form) (NCBI ptt file) 133, 209
CAC2022 moaB Molybdopterin biosynthesis enzyme, moaB (NCBI ptt file) 209, 282
CAC2025 CAC2025 Hypothetical protein (NCBI ptt file) 209, 282
CAC2182 CAC2182 Hypothetical protein (NCBI ptt file) 209, 348
CAC2280 CAC2280 Predicted membrane protein (NCBI ptt file) 134, 268
CAC2446 CAC2446 Hypothetical protein (NCBI ptt file) 27, 209
CAC2505 CAC2505 Uncharacterized membrane protein, YXJN B.subtilis homolog (NCBI ptt file) 134, 176
CAC2518 CAC2518 Extracellular neutral metalloprotease, NPRE (fragment or C-term. domain) (NCBI ptt file) 134, 268
CAC2623 CAC2623 Possible sensorory transduction protein, containing AAA ATPase domain, TPR repeats domain, GGDEF domain and GAF domain (NCBI ptt file) 134, 269
CAC2784 CAC2784 Signal peptidase type IV (NCBI ptt file) 134, 277
CAC2785 CAC2785 Hypothetical protein (NCBI ptt file) 134, 225
CAC3037 ccpA Catabolite control protein, LacI family transcriptional regulator (NCBI ptt file) 11, 209
CAC3279 CAC3279 Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) 209, 261
CAC3290 CAC3290 Iron-regulated ABC-type transporter membrane component (SufB) (NCBI ptt file) 201, 209
CAC3291 CAC3291 Selenocysteine lyase, NifS family (NCBI ptt file) 209, 296
CAC3292 CAC3292 NifU homolog involved in Fe-S cluster formation (NCBI ptt file) 209, 277
CAC3592 CAC3592 Hypothetical protein, CF-27 family (NCBI ptt file) 92, 209
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 CAC2018
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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