Organism : Clostridium acetobutylicum | Module List :
CAC2143 sigD

Sigma factor of SigD/WhiG family (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
phosphatidylserine decarboxylase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
FliA_WhiG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2143
(Mouseover regulator name to see its description)

CAC2143 is regulated by 23 influences and regulates 11 modules.
Regulators for CAC2143 sigD (23)
Regulator Module Operator
CAC0144 41 tf
CAC0284 41 tf
CAC0531 41 tf
CAC1355 41 tf
CAC2052 41 tf
CAC2053 41 tf
CAC2143 41 tf
CAC2934 41 tf
CAC3200 41 tf
CAC3475 41 tf
CAC0032 14 tf
CAC0144 14 tf
CAC0183 14 tf
CAC0197 14 tf
CAC0284 14 tf
CAC0821 14 tf
CAC0863 14 tf
CAC1426 14 tf
CAC1559 14 tf
CAC1766 14 tf
CAC1800 14 tf
CAC2143 14 tf
CAC3475 14 tf

Warning: CAC2143 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
6682 2.40e-04 AAAGagAgggGaga
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6683 1.80e+04 gCtCgC
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6736 3.20e-05 aaGGAGG
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6737 4.80e+03 GGGGTG
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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 CAC2143

CAC2143 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
DNA-directed RNA polymerase specialized sigma subunit cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
phosphatidylserine decarboxylase activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
FliA_WhiG tigr/ tigrfam
Module neighborhood information for CAC2143

CAC2143 has total of 39 gene neighbors in modules 14, 41
Gene neighbors (39)
Gene Common Name Description Module membership
CAC0441 CAC0441 Uncharacterized conserved membrane protein of SANA family (NCBI ptt file) 14, 44
CAC0472 dnaK DnaK protein (heat shock protein), HSP70/DnaK family (NCBI ptt file) 14, 271
CAC0473 dnaK DnaK protein (heat shock protein), C-terminal region has VWA type A domain (NCBI ptt file) 14, 41
CAC0512 CAC0512 Uncharacterized conserved protein, YbhK/UPF0052 family (NCBI ptt file) 41, 343
CAC0513 CAC0513 Uncharacterized conserved protein, similar to B.subtilis yvcL (NCBI ptt file) 41, 154
CAC0531 CAC0531 Transcriptional regulator, RpiR family (NCBI ptt file) 41, 64
CAC0566 CAC0566 Malate dehydrogenase (NCBI ptt file) 14, 22
CAC0821 CAC0821 Transcriptional regulator (TetR/AcrR family) (NCBI ptt file) 14, 271
CAC0823 CAC0823 Predicted membrane protein (NCBI ptt file) 14, 271
CAC0959 clpB ATPase with chaperone activity, two ATP-binding domains (NCBI ptt file) 6, 41
CAC1474 CAC1474 Proline/glycine betaine ABC transport system, periplasmic component (NCBI ptt file) 41, 177
CAC1475 CAC1475 Proline/glycine betaine ABC transport system, ATPase component (NCBI ptt file) 41, 177
CAC1553 CAC1553 Membrane associated sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file) 41, 265
CAC1665 CAC1665 Predicted amidohydrolase (NCBI ptt file) 41, 113
CAC1699 CAC1699 Uncharacterized protein, YfiH family (NCBI ptt file) 14, 172
CAC1700 CAC1700 Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file) 6, 14
CAC1767 CAC1767 Hypothetical protein (NCBI ptt file) 14, 22
CAC1802 infB Translation IF2, GTPase (NCBI ptt file) 14, 213
CAC1964 rpsA Ribosomal protein S1 (NCBI ptt file) 41, 47
CAC2052 CAC2052 DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 41, 64
CAC2053 CAC2053 Hypothetical protein (NCBI ptt file) 41, 64
CAC2142 CAC2142 Hypothetical protein (NCBI ptt file) 6, 14
CAC2143 sigD Sigma factor of SigD/WhiG family (NCBI ptt file) 14, 41
CAC2144 CAC2144 Uncharacterized protein, YPFA B.subtilis ortholog (NCBI ptt file) 14, 41
CAC2145 CAC2145 ATPases involved in chromosome partitioning, MinD family, YLXH B.subtilis ortholog (NCBI ptt file) 14, 41
CAC2146 flhF Flagellar GTP-binding protein, FlhF (NCBI ptt file) 6, 14
CAC2262 addA ATP-dependent exonuclease (exonuclease V) synthesis protein AddA (helicase and exonuclease domains) (NCBI ptt file) 14, 159
CAC2354 CAC2354 Nifs family aminotransferase (NCBI ptt file) 41, 279
CAC2458 CAC2458 2-oxoacid ferredoxin oxidoreductase, beta subunit (NCBI ptt file) 41, 200
CAC2542 CAC2542 FAD/FMN-containing dehydrogenase (NCBI ptt file) 41, 265
CAC2543 etfA Electron-transferring flavoprotein large subunit (NCBI ptt file) 41, 363
CAC2544 etfB Electron-transferring flavoprotein small subunit (NCBI ptt file) 41, 291
CAC2625 CAC2625 Predicted membrane protein (NCBI ptt file) 41, 113
CAC2638 lonB Lon-like ATP-dependent protease (NCBI ptt file) 41, 177
CAC2685 CAC2685 Trehalose/maltose hydrolase (phosphorylase) (NCBI ptt file) 6, 14
CAC3030 CAC3030 Hypothetical protein (NCBI ptt file) 41, 265
CAC3080 CAC3080 Hypothetical protein (NCBI ptt file) 39, 41
CAC3475 CAC3475 Transcriptional regulator, merR family (NCBI ptt file) 14, 320
CAC3658 CAC3658 Uncharacterized conserved membrane protein, SapB/MtgC family (NCBI ptt file) 41, 272
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 CAC2143
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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