Dataset: cluster analysis - Carbonate Organic Matrix proteins

Name: Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project)
Published: 2014-10-29
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.536485.1

Project:

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

Program:

Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)

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)

Version:

Version Date:

2014-10-29

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project)

Abstract:

This dataset includes results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2014-10-29	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.536485.1	2022-05-18

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

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

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.

Data Files

File
SI_Table2.csv (Comma Separated Values (.csv), 131.92 KB) MD5:eef20978ad572b1e7ea5e6751c9a006d Primary data file for dataset ID 536485

Supplemental Files

File

SI_Table_2_references.csv

(Comma Separated Values (.csv), 17.34 KB)
MD5:bc997b3b68e1f4363701c99256fca7c9

Complete reference information for "Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin" dataset (dataset 536485; PI: Falkowski).

The "abbrev" column contains the abbreviated reference as cited in dataset 536485.

The "full_reference" column contains the complete citation for that paper.

SI_Table_2_sequence_codes.csv

(Comma Separated Values (.csv), 1.68 KB)
MD5:b3968320952b0f70c9409d1b32496fa9

Full sequences for those abbreviated in the "detection_type" column of "Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin" dataset (dataset 536485; PI: Falkowski).

The "code" column contains the sequence code as listed in dataset 536485.

The "sequence" column contains the full sequence.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Emerging Frontiers Division	EF-1041143

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
lab_Falkowski		2010-09-01	Rutgers_New_Brunswick	Paul G. Falkowski (Principal Investigator)	data info

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
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
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
genus	Genus name.	text	genus
group_num	Group number.	unitless	no_bcodmo_term
ID1	The accession number, author's assigned protein number, or other note about a designator for the individual protein.	text	no_bcodmo_term
protein_name	Name of the protein.	text	no_bcodmo_term
reference	Reference paper. Refer to Supplemental Files for full citations.	text	reference_paper
species	Species name.	text	species
taxon	Taxonomic grouping (coral, echinoderm, or mollusk).	text	taxon
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

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Dataset: cluster analysis - Carbonate Organic Matrix proteins