Dataset: cluster analysis - Carbonate Organic Matrix proteins
Deployment: lab_Falkowski

Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin.

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/536485

Principal Investigator:

Paul G. Falkowski (Rutgers University, Rutgers IMCS)

Co-Principal Investigator:

Yair Rosenthal (Rutgers University)

Oscar M.E. Schofield (Rutgers University)

Robert M. Sherrell (Rutgers University)

Contact:

Paul G. Falkowski (Rutgers University, Rutgers IMCS)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals (CROA)

Current State:

Final no updates expected

Version:

31 Oct 2014

Version Date:

2014-10-31

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Description

Cluster analysis and gene ontology to compare ~1500 proteins, from over 100 studies, extracted from calcium carbonates in stony corals, bivalve and gastropod mollusks, and adult and larval sea urchins. This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014. Refer to Drake et al. (2014) for more information on methodology and results.

Methods & Sampling

Dataset acquisition description

Methodology described in Drake et al. 2014:
Sequences from over 100 biomineral proteome studies were grouped by hierarchical clustering using the CD-HIT suite web server (Li and Godzik, 2006; Huang et al., 2010; http://weizhong-lab.ucsd.edu/cd-hit/) and assigned gene ontology (GO) terms using Blast2Go software (Conesa et al., 2005). Although 1531 proteins reduced to 1051 clusters at 30% similarity, only 64 clusters showed sequence similarity across phyla. Studies published from the 1990s through June 2013, using N-terminal and mass spectrometry COM sequencing, RT-PCR, or GO and KEGG annotation of genomic and transcriptomic data sets are included. Mass spectrometry sequences were excluded if the experimental data were compared with gene models from a different species.

This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014:
Proteins from coral, mollusk, and sea urchin direct COM sequencing, RT-PCR, or GO and KEGG annotation. 1076 proteins, including redundancy when noted by multiple sources, reduced to 1031 non-redundant sequences.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes:
- Replaced blanks with 'nd' to indicate 'no data'.
- Replaced alpha symbols with the word "alpha" and beta symbols with "beta".
- Created code list ("SI_Table_2_sequence_codes.csv") for long sequences contained in the 'detection_type' column.
- Created reference list ("SI_Table_2_references.csv") for full references of names in the 'reference' column.

More information about this dataset deployment

Funding

Award Number	Funding Source
EF-1041143	NSF Emerging Frontiers Division

Instruments

Mass Spectrometer

Supplied Name: Mass Spec

Supplied Description:

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
protein_name	Name of the protein.	text	no_bcodmo_term
cluster_num	Cluster numbers were assigned to each batch of proteins that clustered together with 30% similarity or higher based on a clustering method using the CD-HIT suite web server. This was done progressively from 100% sequence similarity down to 30% with the cluster numbers carrying through. However, if a protein showed 30% similarity to another batch of proteins, then, for the final cut-off of 30%, the proteins from the previously independent batch were grouped in with the new batch. For instance, Cluster005744 has a cluster_num of 12. That means that it has 30% sequence similarity with proteins from proteins 5955, 00152 1(a), and 19987. In a previous clustering (with a higher similarity cutoff), it also showed sequence similarity with proteins Cluster020987, Cluster020227, and Cluster015890 (so they were previously in cluster #12). However, now proteins Cluster020987, Cluster020227, and Cluster015890 show at least 30% sequence similarity with one of the Cluster000783, Cluster050768, Cluster050003, or lotgi1\|230171 proteins (that were previously assigned to cluster #0). So now since at least 1 protein in cluster #12 is similar to cluster #0, all #12 proteins were assigned to cluster #0.	unitless	no_bcodmo_term
group_num	Group number.	unitless	no_bcodmo_term
genus	Genus name.	text	genus
species	Species name.	text	species
taxon	Taxonomic grouping (coral, echinoderm, or mollusk).	text	taxon
reference	Reference paper. Refer to Supplemental Files for full citations.	text	reference_paper
ID1	The accession number, author's assigned protein number, or other note about a designator for the individual protein.	text	no_bcodmo_term
detection_type	Method used to sequence the protein.The strings of letters are the individual peptide sequences detected by LC-MS/MS.	text	no_bcodmo_term
type	Indicates if the protein can be assigned the name of a type of protein based on BLAST similarity. Also contains notes, such as if the protein was assigned its own accession number but was the same protein as found in another row.	text	no_bcodmo_term

Database

Contribute Data

Dataset: cluster analysis - Carbonate Organic Matrix proteins
Deployment: lab_Falkowski

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: cluster analysis - Carbonate Organic Matrix proteinsDeployment: lab_Falkowski

Dataset acquisition description

Dataset Processing Description

Dataset: cluster analysis - Carbonate Organic Matrix proteins
Deployment: lab_Falkowski