Organism : Methanococcus maripaludis S2 | Module List :
MMP1346

basic helix-loop-helix dimerization domain-containing protein

CircVis
Functional Annotations (2)
Function System
Predicted phosphotransacetylase cog/ cog
methan_mark_4 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1346
(Mouseover regulator name to see its description)

MMP1346 is regulated by 8 influences and regulates 0 modules.
Regulators for MMP1346 (8)
Regulator Module Operator
H2 49 ef
MMP0460 49 tf
MMP0499
MMP1065		 49 combiner
MMP0031
MMP0402		 67 combiner
MMP0031
MMP1704		 67 combiner
MMP0607
MMP1442		 67 combiner
MMP1137 67 tf
MMP1210
MMP1704		 67 combiner

Warning: MMP1346 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
759 1.20e+00 tagATatattGgtGa
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760 1.90e+01 caAgTcTGgTGg
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795 3.10e+03 GGGCGA
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796 1.70e+04 CTGcGGAG
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935 9.60e+02 cCgCcgtgAaC
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936 7.30e+03 CcAccaTTGtaaGc
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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 MMP1346

MMP1346 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted phosphotransacetylase cog/ cog
methan_mark_4 tigr/ tigrfam
Module neighborhood information for MMP1346

MMP1346 has total of 87 gene neighbors in modules 49, 67, 142
Gene neighbors (87)
Gene Common Name Description Module membership
Antisense_13 None 49, 129
Antisense_24 None 5, 49, 90
Antisense_6 None 52, 67
MMP0008 DP1 DNA polymerase II small subunit 22, 75, 142
MMP0017 hypothetical protein MMP0017 67, 142
MMP0019 hypothetical protein MMP0019 14, 104, 142
MMP0020 nickel responsive regulator 49, 123
MMP0021 hypothetical protein MMP0021 14, 142
MMP0035 hypothetical protein MMP0035 23, 67
MMP0036 tfe transcription initiation factor E subunit alpha 49, 87, 92, 129
MMP0063 argB acetylglutamate kinase 49, 151
MMP0084 hypothetical protein MMP0084 49, 106
MMP0108 ABC-type Iron(III)-binding periplasmic protein precursor 41, 67, 95
MMP0113 hypothetical protein MMP0113 23, 75, 142
MMP0119 birA biotin--acetyl-CoA-carboxylase ligase 1, 75, 142
MMP0120 hypothetical protein MMP0120 55, 142
MMP0124 membrane-bound metal-dependent hydrolase 14, 67
MMP0202 permease 52, 67
MMP0203 hypothetical protein MMP0203 52, 67
MMP0204 hypothetical protein MMP0204 67, 99
MMP0225 gldA glycerol dehydrogenase 117, 142
MMP0227 nrdD anaerobic ribonucleoside-triphosphate reductase 15, 67
MMP0239 hypothetical protein MMP0239 1, 49, 75, 106
MMP0262 hypothetical protein MMP0262 52, 67
MMP0268 truA tRNA pseudouridine synthase A 49, 51
MMP0274 hypE hydrogenase expression/formation protein HypE 67, 70
MMP0277 TraB family protein 49, 90
MMP0279 mptG beta-ribofuranosylaminobenzene 5'-phosphate synthase family protein 49, 90
MMP0280 hisI phosphoribosyl-AMP cyclohydrolase 67, 90
MMP0302 hypothetical protein MMP0302 49, 90
MMP0307 hypothetical protein MMP0307 33, 49, 153
MMP0322 rfcB replication factor C large subunit 23, 67
MMP0324 hypothetical protein MMP0324 62, 142
MMP0341 pycA pyruvate carboxylase subunit A 67, 86, 120
MMP0446 nitrogen fixation-like protein 52, 67
MMP0488 low molecular weight phosphotyrosine protein phosphatase 52, 67
MMP0489 hypothetical protein MMP0489 52, 67
MMP0544 MoaA/nifB/pqqE family protein 55, 142
MMP0545 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein 55, 142
MMP0562 hypothetical protein MMP0562 49, 124
MMP0617 radB DNA repair and recombination protein RadB 52, 67
MMP0643 hypothetical protein MMP0643 49, 65
MMP0648 rtcA RNA 3'-terminal-phosphate cyclase 67, 146
MMP0682 hypothetical protein MMP0682 67, 92
MMP0725 putative integral membrane protein 49, 75, 90, 151
MMP0727 uvrB excinuclease ABC subunit B 49, 142
MMP0728 uvrC excinuclease ABC subunit C 90, 142
MMP0742 hypothetical protein MMP0742 23, 49
MMP0760 hypothetical protein MMP0760 22, 67, 92
MMP0811 hypothetical protein MMP0811 52, 67
MMP0902 hypothetical protein MMP0902 12, 49, 55
MMP0918 asnB glutamine-hydrolyzing asparagine synthase 49, 115
MMP0986 thyA thymidylate synthase 104, 142
MMP0993 XRE family transcriptional regulator 67, 144
MMP0994 hypothetical protein MMP0994 67, 144, 153
MMP1009 pyrC dihydroorotase 22, 142
MMP1062 hypothetical protein MMP1062 142, 144
MMP1079 glycosyl transferase family protein 64, 67
MMP1080 group 1 glycosyl transferase 14, 142
MMP1120 ATPase-like ATP-binding protein 52, 67
MMP1123 radical SAM domain-containing protein 64, 67
MMP1141 ATP-dependent helicase 75, 142
MMP1218 hypothetical protein MMP1218 12, 46, 49
MMP1228 hypothetical protein MMP1228 4, 22, 142
MMP1235 moaE molybdopterin biosynthesis MoaE 49, 55, 106, 117, 150
MMP1236 hypothetical protein MMP1236 22, 55, 117, 142, 152
MMP1264 hypothetical protein MMP1264 104, 142, 157
MMP1282 hypothetical protein MMP1282 49, 102, 106, 150
MMP1283 hypothetical protein MMP1283 49, 102, 150
MMP1290 GTP-binding protein 49, 115
MMP1343 hypothetical protein MMP1343 49, 151
MMP1345 undecaprenyl pyrophospahte synthetase-like protein 49, 111
MMP1346 basic helix-loop-helix dimerization domain-containing protein 49, 67, 142
MMP1372 manB phosphomannomutase 49, 94, 152
MMP1398 dapE diaminopimelate aminotransferase 22, 142
MMP1430 cation transporter 49, 115
MMP1431 2pgk 2-phosphoglycerate kinase 49, 51
MMP1485 moaB molybdenum cofactor biosynthesis protein 104, 142
MMP1551 ffh signal recognition particle protein Srp54 49, 55, 83
MMP1597 phosphatidylglycerophosphatase A 22, 142, 144
MMP1603 ferredoxin 12, 49
MMP1606 flavoprotein:DNA/pantothenate metabolism flavoprotein 1, 13, 49
MMP1607 hypothetical protein MMP1607 49, 55, 83
MMP1686 cbf5 H/ACA RNA-protein complex component Cbf5p 22, 67
Unanno_14 None 52, 67
Unanno_42 None 49, 90
Unanno_62 None 49, 90
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 MMP1346
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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