Organism : Methanococcus maripaludis S2 | Module List :
MMP1646

hypothetical protein MMP1646

CircVis
Functional Annotations (3)
Function System
Predicted transcription factor, homolog of eukaryotic MBF1 cog/ cog
sequence-specific DNA binding go/ molecular_function
TIGR00270 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1646
(Mouseover regulator name to see its description)

MMP1646 is regulated by 10 influences and regulates 36 modules.
Regulators for MMP1646 (10)
Regulator Module Operator
MMP0052 96 tf
MMP0052
MMP1304
96 combiner
MMP0097
MMP1052
96 combiner
MMP0460 96 tf
MMP1015 96 tf
MMP1447 96 tf
MMP0033
MMP0629
136 combiner
MMP0209
MMP1023
136 combiner
MMP0465 136 tf
MMP0791 136 tf

Warning: MMP1646 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
849 1.70e+02 gAGGTGc
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850 1.60e+04 CCcTGCc
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923 4.70e+03 tagtAaaGTt.CcgC
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924 9.00e+03 GAGGCaCG
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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 MMP1646

MMP1646 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted transcription factor, homolog of eukaryotic MBF1 cog/ cog
sequence-specific DNA binding go/ molecular_function
TIGR00270 tigr/ tigrfam
Module neighborhood information for MMP1646

MMP1646 has total of 52 gene neighbors in modules 96, 136
Gene neighbors (52)
Gene Common Name Description Module membership
MMP0060 rplX 50S ribosomal protein LX 61, 96, 138
MMP0061 aIF6 translation initiation factor IF-6 8, 61, 96, 138
MMP0062 50S ribosomal protein L31e 61, 77, 96, 128, 138
MMP0075 abortive infection protein 96, 136
MMP0087 hmgA hydroxymethylglutaryl-coenzyme A reductase:3-hydroxy-3-methylglutaryl coenzyme A reductase 39, 136
MMP0088 hemA glutamyl-tRNA reductase 39, 136
MMP0163 arsA arsenite-activated ATPase ArsA 16, 96
MMP0164 cbiX(s) sirohydrochlorin cobaltochelatase 39, 136
MMP0242 hypothetical protein MMP0242 8, 39, 96
MMP0245 pfdB prefoldin subunit beta 96, 138
MMP0317 hypothetical protein MMP0317 77, 96
MMP0350 hexapeptide repeat-containing transferase 80, 96
MMP0370 hypothetical protein MMP0370 77, 96
MMP0429 hypothetical protein MMP0429 64, 136
MMP0443 rps24e 30S ribosomal protein S24e 3, 51, 96, 97
MMP0572 slyD FKBP-type peptidylprolyl isomerase 11, 96
MMP0578 aroQ chorismate mutase 11, 18, 96, 138
MMP0644 cation diffusion facilitator family transporter 39, 136
MMP0645 mdh malate dehydrogenase 8, 39, 136
MMP0646 hypothetical protein MMP0646 39, 136
MMP0657 hypothetical protein MMP0657 8, 29, 96
MMP0668 hypothetical protein MMP0668 3, 96, 105
MMP0874 SAM-binding motif-containing protein 39, 136
MMP0875 slpB S layer protein 39, 136
MMP0887 stress responsive alpha-beta barrel domain-containing protein 40, 136
MMP0888 cobalt transport protein CbiN 39, 136
MMP0889 cobalt transport protein CbiM 39, 136
MMP0917 dapF diaminopimelate epimerase 107, 136
MMP0946 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 8, 81, 96
MMP0965 formylmethanofuran dehydrogenase subunit E-like protein 8, 39, 136
MMP1013 carB carbamoyl-phosphate synthase large subunit 77, 96
MMP1035 hypothetical protein MMP1035 77, 136
MMP1036 hypothetical protein MMP1036 77, 136
MMP1113 transketoloase, C terminal half 96, 120
MMP1147 rpl37e 50S ribosomal protein L37e 18, 96, 138
MMP1175 hypothetical protein MMP1175 14, 136
MMP1176 putative iron transport system substrate-binding protein, N-term half 39, 136
MMP1177 putative iron transport system substrate-binding protein, C-term half 39, 136
MMP1178 periplasmic binding protein 39, 136
MMP1181 iron transport system binding protein 39, 136
MMP1182 transport system permease 39, 136
MMP1183 iron ABC transporter ATPase subunit 39, 136
MMP1208 aIF2_gamma translation initiation factor IF-2 subunit gamma 20, 61, 96
MMP1254 purM phosphoribosylaminoimidazole synthetase 96, 120
MMP1260 hypothetical protein MMP1260 40, 96
MMP1401 ef1B elongation factor 1-beta 61, 96, 97, 105
MMP1403 rpl22p 50S ribosomal protein L22P 3, 61, 92, 96, 97, 105
MMP1433 rpl11p 50S ribosomal protein L11P 96, 97, 105
MMP1515 hsp60 chaperonin GroEL 77, 96
MMP1646 hypothetical protein MMP1646 96, 136
MMP1699 hypothetical protein MMP1699 77, 136
Unanno_9 None 39, 136
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 MMP1646
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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