Organism : Clostridium acetobutylicum | Module List :
CAC3647 abrB

Transition state regulatory protein AbrB (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3647
(Mouseover regulator name to see its description)

CAC3647 is regulated by 23 influences and regulates 14 modules.
Regulators for CAC3647 abrB (23)
Regulator Module Operator
CAC0457 281 tf
CAC0977 281 tf
CAC1340 281 tf
CAC1536 281 tf
CAC1719 281 tf
CAC1941 281 tf
CAC2113 281 tf
CAC2495 281 tf
CAC2962 281 tf
CAC3037 281 tf
CAC3611 281 tf
CAC3647 281 tf
CAC0115 304 tf
CAC0707 304 tf
CAC0977 304 tf
CAC1426 304 tf
CAC1536 304 tf
CAC1719 304 tf
CAC1950 304 tf
CAC2476 304 tf
CAC2966 304 tf
CAC3104 304 tf
CAC3647 304 tf

Warning: CAC3647 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
7214 4.40e-05 .acctCCT.ttat
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7215 8.70e+03 gAgGAgGagA
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7260 7.50e-04 gTaatTaaggAGGtg
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7261 7.30e-01 GGAaGAAgg
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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 CAC3647

CAC3647 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
Module neighborhood information for CAC3647

CAC3647 has total of 50 gene neighbors in modules 281, 304
Gene neighbors (50)
Gene Common Name Description Module membership
CAC0126 CAC0126 Uncharacterized conserved protein, YbaB family (NCBI ptt file) 10, 281
CAC0127 recR Recombination protein (recR) (NCBI ptt file) 32, 281
CAC0128 CAC0128 Hypothetical protein (NCBI ptt file) 281, 304
CAC0129 bofA BofA B.subtilis ortholog, SigmaK-factor processing regulatory protein (NCBI ptt file) 77, 304
CAC0228 CAC0228 Hypothetical protein (NCBI ptt file) 304, 322
CAC0528 CAC0528 ABC transporter, ATPase component (two ATPase domains) (NCBI ptt file) 249, 281
CAC0546 CAC0546 Uncharacterized membrane protein, homolog of Methanobacterium (2621593) (NCBI ptt file) 95, 304
CAC0716 smpB TmRNA-binding protein SmpB (NCBI ptt file) 53, 304
CAC0730 CAC0730 Predicted permease (NCBI ptt file) 146, 304
CAC0771 CAC0771 Cobalamin biosynthesis protein CbiM (NCBI ptt file) 262, 304
CAC0868 CAC0868 Predicted membrane protein (NCBI ptt file) 118, 304
CAC0965 CAC0965 1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file) 58, 281
CAC0992 CAC0992 Hypothetical protein (NCBI ptt file) 73, 281
CAC1065 CAC1065 Uncharacterized protein, related stage III sporulation protein AH of Bacillus sp. (NCBI ptt file) 59, 304
CAC1239 CAC1239 Predicted membrane protein (NCBI ptt file) 172, 281
CAC1240 maf Maf protein ortholog, putative inhibitor of septum formation (NCBI ptt file) 229, 281
CAC1251 rodA Cell division protein, rodA/ftsW/spoVE family (NCBI ptt file) 76, 281
CAC1274 rpsT Ribosomal protein S20 (NCBI ptt file) 281, 304
CAC1334 CAC1334 Fe-S oxidoreductase of MoeA/NarA subfamily (NCBI ptt file) 214, 304
CAC1654 CAC1654 Zn-dependent metalloprotease, insulinase family (NCBI ptt file) 105, 281
CAC1719 rpoZ RNA polymerase-associated protein RpoZ, omega subunit (YLOH B.subtilis ortholog) (NCBI ptt file) 172, 281
CAC1740 CAC1740 Uncharcaterized membrane protein, YLBJ B.subtilis homolog (NCBI ptt file) 59, 304
CAC1762 rnh Ribonuclease HII (NCBI ptt file) 116, 281
CAC1785 topA Topoisomerase I (NCBI ptt file) 79, 281
CAC2030 CAC2030 Hypothetical protein (NCBI ptt file) 270, 281
CAC2094 efp Translation elongation factor P (NCBI ptt file) 152, 281
CAC2110 CAC2110 GAF domain-containing protein (NCBI ptt file) 233, 304
CAC2183 CAC2183 Uncharacterized protein, posible homoloh of YJFB B. subtilis (NCBI ptt file) 281, 286
CAC2228 CAC2228 Hypothetical protein (NCBI ptt file) 76, 281
CAC2299 hflX Predicted GTPase, HflX (NCBI ptt file) 35, 304
CAC2476 CAC2476 Uncharacterized protein, homolog of Spirochaeta aurantia (gi:152901) (NCBI ptt file) 38, 304
CAC2477 CAC2477 Hypothetical protein (NCBI ptt file) 38, 304
CAC2641 tig FKBP-type peptidyl-prolyl cis-transisomerase (trigger factor) (NCBI ptt file) 304, 329
CAC2665 CAC2665 Xanthosine triphosphate pyrophosphatase, HAM1-like protein (NCBI ptt file) 64, 281
CAC2671 CAC2671 Glu-tRNAGln amidotransferase subunit C (NCBI ptt file) 79, 281
CAC2713 CAC2713 AT-rich DNA-binding protein (NCBI ptt file) 76, 281
CAC2769 ppiB Peptidyl-prolyl cis-transisomerase, cyclophilin family (NCBI ptt file) 254, 281
CAC2864 atpC FoF1-type ATP synthase epsilon subunit (NCBI ptt file) 304, 335
CAC2865 atpD FoF1-type ATP synthase beta subunit (NCBI ptt file) 59, 304
CAC2870 atpE FoF1-type ATP synthase C subunit (NCBI ptt file) 59, 304
CAC2888 rpmE 50S ribosomal protein L31 (NCBI ptt file) 38, 304
CAC3038 ileS Isoleucyl-tRNA synthetase (NCBI ptt file) 146, 304
CAC3104 rpoA DNA-dependent RNA polymerase alpha subunit (NCBI ptt file) 8, 304
CAC3113 seqY Preprotein translocase subunit SecY (NCBI ptt file) 292, 304
CAC3122 rplX Ribosomal protein L24 (NCBI ptt file) 255, 304
CAC3210 CAC3210 Predicted RNA-binding protein, YABO B.subtilis ortholog (NCBI ptt file) 215, 281
CAC3287 CAC3287 Predicted membrane protein (NCBI ptt file) 105, 281
CAC3647 abrB Transition state regulatory protein AbrB (NCBI ptt file) 281, 304
CAC3700 CAC3700 Hypothetical protein, CF-44 family (NCBI ptt file) 162, 304
CAC3739 rpmH L34 (NCBI ptt file) 201, 281
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 CAC3647
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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