Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1369

Short-chain dehydrogenase/reductase SDR (NCBI)

CircVis
Functional Annotations (3)
Function System
Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) cog/ cog
metabolic process go/ biological_process
oxidoreductase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1369
(Mouseover regulator name to see its description)

RSP_1369 is regulated by 22 influences and regulates 0 modules.
Regulators for RSP_1369 (22)
Regulator Module Operator
RSP_0014 215 tf
RSP_0547 215 tf
RSP_0611 215 tf
RSP_0623 215 tf
RSP_1191 215 tf
RSP_1518 215 tf
RSP_1776 215 tf
RSP_3385 215 tf
RSP_3680 215 tf
RSP_0327 126 tf
RSP_0611 126 tf
RSP_0755 126 tf
RSP_1040 126 tf
RSP_1550 126 tf
RSP_1663 126 tf
RSP_1776 126 tf
RSP_2165 126 tf
RSP_2425 126 tf
RSP_2572 126 tf
RSP_2606 126 tf
RSP_2888 126 tf
RSP_3731 126 tf

Warning: RSP_1369 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
7972 9.10e-08 atCtGca.CaTCTTgacGATAAcC
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7973 5.10e-02 ccttCtGaTcC
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8150 1.90e+01 ctGaTcgacATCGACgAgctcaA
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8151 1.20e+04 aaCtGACGGTCGa
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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_1369

RSP_1369 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) cog/ cog
metabolic process go/ biological_process
oxidoreductase activity go/ molecular_function
Module neighborhood information for RSP_1369

RSP_1369 has total of 49 gene neighbors in modules 126, 215
Gene neighbors (49)
Gene Common Name Description Module membership
RSP_0014 RSP_0014 transcriptional regulator, TetR family (NCBI) 91, 215
RSP_0327 nnrR Crp-Fnr regulatory protein (NnrR) (NCBI) 4, 126
RSP_0337 RSP_0337 possible phospodiesterase (NCBI) 120, 215
RSP_0338 RSP_0338 hypothetical protein (NCBI) 120, 215
RSP_0363 RSP_0363 hypothetical protein (NCBI) 215, 218
RSP_0406 RSP_0406 periplasmic sensor diguanylate cyclase (GGDEF) (NCBI) 126, 175
RSP_0586 RSP_0586 probable nicotinate-nucleotide adenylyltransferase (NCBI) 7, 215
RSP_0782 RSP_0782 Ppx/GppA phosphatase (NCBI) 215, 240
RSP_0784 RSP_0784 putative acetyltransferase, GNAT family (NCBI) 215, 240
RSP_0814 RSP_0814 Acetyltransferase (NCBI) 215, 248
RSP_0876 RSP_0876 Chromosome segregation protein SMC2 (NCBI) 126, 302
RSP_0878 RSP_0878 putative acetyltransferase protein (NCBI) 126, 294
RSP_0987 RSP_0987 Putative transporter, RarD family, DMT superfamily (NCBI) 84, 126
RSP_1040 RSP_1040 transcriptional regulator, ArsR family (NCBI) 98, 126
RSP_1189 wcaJ sugar transferase (NCBI) 47, 215
RSP_1190 RSP_1190 hypothetical protein (NCBI) 215, 368
RSP_1191 RSP_1191 transcriptional regulator, MarR family (NCBI) 215, 368
RSP_1192 RSP_1192 None 215, 368
RSP_1214 RSP_1214 putative branched-chain amino acid aminotransferase (NCBI) 215, 381
RSP_1275 RSP_1275 Crp-Fnr family transciptional regulator (NCBI) 215, 340
RSP_1276 RSP_1276 hypothetical protein (NCBI) 215, 368
RSP_1287 RSP_1287 ABC branched chain amino acid family transporter, ATPase subunit (NCBI) 215, 263
RSP_1361 RSP_1361 hypothetical protein (NCBI) 126, 174
RSP_1369 RSP_1369 Short-chain dehydrogenase/reductase SDR (NCBI) 126, 215
RSP_1371 RSP_1371 putative 2-dehydro-3-deoxygalactonokinase (NCBI) 126, 136
RSP_1511 RSP_1511 hypothetical protein (NCBI) 215, 372
RSP_1663 RSP_1663 putative transcriptional regulator, LacI family (NCBI) 81, 126
RSP_1830 surf-1 Surf1 protein (NCBI) 126, 356
RSP_1835 RSP_1835 Putative FAD dependent oxidoreductase (NCBI) 126, 322
RSP_1861 RSP_1861 probable dihydroneopterin aldolase (NCBI) 215, 326
RSP_1896 RSP_1896 probable guanine deaminase (NCBI) 63, 126
RSP_1927 RSP_1927 hypothetical protein (NCBI) 126, 331
RSP_2017 RSP_2017 hypothetical protein (NCBI) 23, 126
RSP_2165 putR transcriptional regulator, AsnC family (NCBI) 107, 126
RSP_2168 RSP_2168 hypothetical protein (NCBI) 126, 175
RSP_2312 RSP_2312 hypothetical protein (NCBI) 215, 231
RSP_2375 RSP_2375 hypothetical protein (NCBI) 215, 366
RSP_2382 RSP_2382 hypothetical protein (NCBI) 215, 294
RSP_2390 acuC1 putative Acetoin utilization protein (NCBI) 126, 340
RSP_2391 RSP_2391 2'-5' RNA ligase (NCBI) 126, 215
RSP_2634 ccmH Cytochrome c maturation protein, CcmH (NCBI) 215, 368
RSP_2678 RSP_2678 hypothetical protein (NCBI) 215, 340
RSP_2788 RSP_2788 hypothetical protein (NCBI) 36, 215
RSP_2914 RSP_2914 Nucleoside hydrolase (NCBI) 126, 309
RSP_3012 RSP_3012 Probable transposase (NCBI) 77, 126
RSP_3023 RSP_3023 hypothetical protein (NCBI) 215, 303
RSP_3402 RSP_3402 multisensor diguanylate cyclase/phosphodiesterase (NCBI) 17, 215
RSP_3564 RSP_3564 Generic methyltransferase (NCBI) 7, 215
RSP_3680 RSP_3680 transcriptional regulator, TetR family (NCBI) 143, 215
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_1369
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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