Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2134 ccdA

putative cytochrome c-type biogenesis protein CcdA (NCBI)

CircVis
Functional Annotations (3)
Function System
Cytochrome c biogenesis protein cog/ cog
membrane go/ cellular_component
cytochrome complex assembly go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2134
(Mouseover regulator name to see its description)

RSP_2134 is regulated by 17 influences and regulates 0 modules.
Regulators for RSP_2134 ccdA (17)
Regulator Module Operator
RSP_0394 242 tf
RSP_0623 242 tf
RSP_0641 242 tf
RSP_1014 242 tf
RSP_1032 242 tf
RSP_1243 242 tf
RSP_1550 242 tf
RSP_1915 242 tf
RSP_3055 242 tf
RSP_3226 242 tf
RSP_0443 2 tf
RSP_0601 2 tf
RSP_0698 2 tf
RSP_1866 2 tf
RSP_2410 2 tf
RSP_2888 2 tf
RSP_3664 2 tf

Warning: RSP_2134 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
7726 2.70e+00 CGTccatCCGGCtCAaCCtCcGGA
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7727 1.40e+02 TAgGaaaGcgaCAAaGagGGa
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8202 1.90e+02 TCcGGCaGcGG
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8203 3.20e+04 ttcacccAcCgtgAaatGAtG
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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 RSP_2134

RSP_2134 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Cytochrome c biogenesis protein cog/ cog
membrane go/ cellular_component
cytochrome complex assembly go/ biological_process
Module neighborhood information for RSP_2134

RSP_2134 has total of 45 gene neighbors in modules 2, 242
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0119 RSP_0119 PA-phosphatase related phosphoesterase (NCBI) 2, 4
RSP_0176 RSP_0176 Dihydroxyacid dehydratase/phosphogluconate dehydratase (NCBI) 83, 242
RSP_0177 RSP_0177 FAD/FMN-containing dehydrogenases (NCBI) 242, 308
RSP_0215 RSP_0215 hypothetical protein (NCBI) 242, 288
RSP_0354 RSP_0354 hypothetical protein (NCBI) 242, 285
RSP_0440 sufB putative SufB (NCBI) 2, 289
RSP_0521 RSP_0521 putative Zn-containing dehydrogenase (NCBI) 217, 242
RSP_0558 RSP_0558 Possible ribosomal protein L11 methyltransferase (NCBI) 2, 218
RSP_0599 RSP_0599 Probable DNA/pantothenate metabolism flavoprotein (NCBI) 242, 381
RSP_0654 RSP_0654 possible transporter, DMT superfamily (NCBI) 33, 242
RSP_0708 RSP_0708 NUDIX hydrolase (NCBI) 242, 381
RSP_0730 RSP_0730 hypothetical protein (NCBI) 2, 54
RSP_0761 RSP_0761 hypothetical protein (NCBI) 2, 162
RSP_0785 RSP_0785 Putative heat shock protein DnaJ (NCBI) 13, 242
RSP_0801 RSP_0801 deacetylase / probable acetylpolyamine aminohydrolase (NCBI) 168, 242
RSP_0969 RSP_0969 putative integral membrane protein (NCBI) 2, 280
RSP_1000 RSP_1000 hypothetical protein (NCBI) 2, 285
RSP_1096 RSP_1096 putative zinc protease (NCBI) 2, 184
RSP_1121 RSP_1121 acetyl transferase, Isoleucine patch superfamily (NCBI) 133, 242
RSP_1122 RSP_1122 hypothetical protein (NCBI) 128, 242
RSP_1184 RSP_1184 ribonuclease BN (NCBI) 83, 242
RSP_1185 RSP_1185 hypothetical protein (NCBI) 242, 310
RSP_1322 fhlB flagellar biosynthesis pathway, component FlhB (NCBI) 23, 242
RSP_1363 mepA putative murein endopeptidase transmembrane protein (NCBI) 82, 242
RSP_1409 RSP_1409 Beta-Ig-H3/Fasciclin (NCBI) 2, 161
RSP_1410 RSP_1410 hypothetical protein (NCBI) 2, 30
RSP_1411 RSP_1411 putative membrane protein (NCBI) 2, 4
RSP_1807 RSP_1807 hypothetical protein (NCBI) 2, 287
RSP_2012 RSP_2012 NUDIX hydrolase, MutT (NCBI) 175, 242
RSP_2132 RSP_2132 Protein of unknown function UPF0033 (NCBI) 2, 53
RSP_2134 ccdA putative cytochrome c-type biogenesis protein CcdA (NCBI) 2, 242
RSP_2271 RSP_2271 hypothetical protein (NCBI) 2, 294
RSP_2609 dcd putative deoxycytidine triphosphate deaminase (NCBI) 2, 98
RSP_2660 RSP_2660 Ribonuclease BN family protein (NCBI) 117, 242
RSP_2849 RSP_2849 hypothetical membrane protein (NCBI) 2, 4
RSP_2857 RSP_2857 D-beta-hydroxybutyrate dehydrogenase (NCBI) 242, 278
RSP_2929 RSP_2929 putative disulfide bond formation protein DsbB (NCBI) 2, 331
RSP_3055 RSP_3055 transcriptional regulator, MarR family (NCBI) 176, 242
RSP_3067 RSP_3067 hypothetical protein (NCBI) 2, 19
RSP_3120 RSP_3120 hypothetical protein (NCBI) 2, 42
RSP_3327 RSP_3327 possible Rhomboid family membrane protein (NCBI) 2, 280
RSP_3423 xthA1 Probable exodeoxyribonuclease III (NCBI) 2, 280
RSP_3541 RSP_3541 hypothetical protein (NCBI) 103, 242
RSP_3584 RSP_3584 hypothetical protein (NCBI) 95, 242
RSP_3826 RSP_3826 hypothetical protein (NCBI) 174, 242
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 RSP_2134
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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