Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2012

stage II sporulation protein D-like

CircVis
Functional Annotations (3)
Function System
Sporulation protein and related proteins cog/ cog
sporulation resulting in formation of a cellular spore go/ biological_process
SpoIID_LytB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2012
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2012!

Warning: Synpcc7942_2012 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1565 7.60e-01 acTcagccaAC.CtagAGtgc
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1566 1.80e+00 atTggctgc.CATGgctAcgatCc
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1567 6.20e+00 CAagt..ccgttgCTtta.cG
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1889 4.40e-02 ATTTgaGa.cTaAa.CAaGTC
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1890 1.30e+00 CAaTttTG
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1891 4.30e-01 gaTgctttAcagTtctT.AttT
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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 Synpcc7942_2012

Synpcc7942_2012 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Sporulation protein and related proteins cog/ cog
sporulation resulting in formation of a cellular spore go/ biological_process
SpoIID_LytB tigr/ tigrfam
Module neighborhood information for Synpcc7942_2012

Synpcc7942_2012 has total of 53 gene neighbors in modules 15, 124
Gene neighbors (53)
Gene Common Name Description Module membership
Synpcc7942_0036 hypothetical protein 15, 58
Synpcc7942_0040 dihydroneopterin aldolase Dihydroneopterin aldolase (EC:4.1.2.25) 15, 124
Synpcc7942_0041 possible tyrosine transporter P-protein (TC 2.A.45.2.1) (IMGterm) 15, 69
Synpcc7942_0057 putative C-3 methyl transferase 15, 113
Synpcc7942_0120 Cytosine/adenosine deaminase-like 124, 134
Synpcc7942_0526 "carbohydrate ABC transporter membrane protein 1, CUT1 family (TC 3.A.1.1.-) (IMGterm)" 15, 124
Synpcc7942_0650 hypothetical protein 15, 124
Synpcc7942_0651 replication restart DNA helicase PriA (IMGterm) 15, 124
Synpcc7942_0672 group2 RNA polymerase sigma factor SigD 15, 124
Synpcc7942_0688 "transcriptional regulator, ArsR family (IMGterm)" 11, 15
Synpcc7942_0914 tRNA-(MS(2)IO(6)A)-hydroxylase-like (EC:1.-) 20, 124
Synpcc7942_0947 "carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-) (IMGterm)" 15, 19
Synpcc7942_0981 hypothetical protein 15, 187
Synpcc7942_1034 Transglutaminase-like 15, 187
Synpcc7942_1111 serine/threonine protein kinase (IMGterm) 15, 124
Synpcc7942_1112 ribosomal large subunit pseudouridine synthase D (EC 5.4.99.-) (IMGterm) 15, 124
Synpcc7942_1193 Phospholipid/glycerol acyltransferase 4, 15
Synpcc7942_1243 cyclic nucleotide-binding domain (cNMP-BD) protein 57, 124
Synpcc7942_1299 hypothetical protein 15, 124
Synpcc7942_1300 5-formyltetrahydrofolate cyclo-ligase (IMGterm) 102, 124
Synpcc7942_1336 hypothetical protein 95, 124
Synpcc7942_1337 Integrins alpha chain 19, 124
Synpcc7942_1360 cell envelope-related transcriptional attenuator (IMGterm) 124, 203
Synpcc7942_1371 magnesium and cobalt transport protein CorA 15, 179
Synpcc7942_1468 "multisubunit sodium/proton antiporter, MrpB subunit (TC 2.A.63.1) (IMGterm)" 78, 124
Synpcc7942_1558 hypothetical protein 15, 124
Synpcc7942_1575 Glycogen debranching enzyme 15, 54
Synpcc7942_1599 hypothetical protein 15, 124
Synpcc7942_1604 hypothetical protein 102, 124
Synpcc7942_1706 hypothetical protein 102, 124
Synpcc7942_1739 "transcriptional regulator, MerR family (IMGterm)" 43, 124
Synpcc7942_1740 UDP-N-acetylmuramate dehydrogenase (EC 1.1.1.158) (IMGterm) 124, 183
Synpcc7942_1773 hypothetical protein 15, 80
Synpcc7942_1788 hypothetical protein 102, 124
Synpcc7942_1869 probable cation efflux system protein 124, 126
Synpcc7942_1889 (1->4)-alpha-D-glucan branching enzyme (IMGterm) 15, 124
Synpcc7942_1893 neutral amino acid ABC transporter ATP-binding protein (IMGterm) 79, 124
Synpcc7942_2000 Penicillin-binding protein 1A (EC:2.4.1.129) 102, 124
Synpcc7942_2011 RNAse Z (EC 3.1.26.11) (IMGterm) 15, 176
Synpcc7942_2012 stage II sporulation protein D-like 15, 124
Synpcc7942_2035 hypothetical protein 3, 15
Synpcc7942_2237 hypothetical protein 20, 124
Synpcc7942_2279 ammonium transporter (TC 1.A.11) (IMGterm) 15, 19
Synpcc7942_2303 Dihydropteroate synthase (EC 2.5.1.15) (IMGterm) 3, 15
Synpcc7942_2311 hypothetical protein 15, 102
Synpcc7942_2328 TPR repeat 15, 183
Synpcc7942_2329 metal dependent phosphohydrolase (IMGterm) 15, 79
Synpcc7942_2414 hypothetical protein 3, 124
Synpcc7942_2464 N-acylglucosamine-6-phosphate 2-epimerase (EC:5.1.3.9) 124, 179
Synpcc7942_2528 hypothetical protein 79, 124
Synpcc7942_2594 hypothetical protein 15, 31
Synpcc7942_2595 hypothetical protein 15, 20
Synpcc7942_2596 probable oxidoreductase 15, 102
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 Synpcc7942_2012
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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