SPD

2019/11/29

Web Site: http://proteome.dc.affrc.go.jp/Soybean/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/spd/

SPD is the database of proteome, transcriptome and metabolome from soybeans under flood stress.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Soybean protein data (gel-based)
  3. Soybean Gel data
  4. Soybean Gel spot data
  5. Soybean protein data (gel-free)
  6. Soybean transciptome data
  7. Soybean metabolites data
  8. Soybean omics data
  9. References
  10. Soybean comparative protein data
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "SPD" data.
File README_e.html (English)
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2.2 Soybean protein data (gel-based)

Data name Soybean protein data (gel-based)
Description of data contents

Soybean protein data collected from samples in different organs, flood conditions and time course, and separated by two-dimensional polyacrylamide gel electrophoresis. See " Soybean gel data" for each gel.
File soybean_based_proteomics_list.zip (270 KB)

Data items are the following:
Data itemDescription
Accession Identified protein accession number
Gel ID Gel ID where the protein is separated
Spot ID Spot ID on thegel
Description Description of the protein
Exp pI Measured isoelectric point of the protein
Exp Mw Measured molecular weight of the protein
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2.3 Soybean Gel data

Data name Soybean Gel data
Description of data contents

Gel data in the experiment where "Soybean protein data (gel-based)" is collected.
File soybean_based_proteomics_gel.zip (6.1 MB)

Data items are the following:
Data itemDescription
Gel ID Gel ID
Condition Experiment sample condition
pI Range of measured isoelectric point in the gel
Mw Range of measured molecular weight in the gel
Identified spots Number of identified spots in the gel
Identified proteins Number of identified proteins in the gel
Gel image Gel image (only in simple search)
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2.4 Soybean Gel spot data

Data name Soybean Gel spot data
Description of data contents

Coordinate, pI and mw data on the gel spot in two-dimensional polyacrylamide gel electrophoresis.
File soybean_based_proteomics_spot.zip (68 KB)

Data items are the following:
Data itemDescription
Gel ID Gel ID
Spot ID Spot ID
X X coordinate on the gel
Y Y coordinate on the gel
pI Protein isoelectric point on the spot
Mw Protein molocular weight on the spot
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2.5 Soybean protein data (gel-free)

Data name Soybean protein data (gel-free)
Description of data contents

Soybean protein data collected from samples in different organs, flood conditions and time course, and measured with mass spectrometer.
File soybean_free_proteomics_info.zip (1.8 MB)

Data items are the following:
Data itemDescription
Accession (Soybean) Protein accession number in soybean
Accession (Arabidopsis) Protein accession number in arabidopsis
Description Description of the protein
Stage Soybean development stage ("Seed" or days after sowing)
Organ Organ of soybean
Organelle Organelle of soybean
Stress Condition of flood stress
Mass Protein molecular weight measured by mass spectrometer
Protein content (mol %) Protein molar concentration in the sample
emPAI Protein emPAI concentration in the sample
Peptides Number of peptides in the sample which match the protein
Score Matching score about the above
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2.6 Soybean transciptome data

Data name Soybean transciptome data
Description of data contents

Samples are collected from soybean in different flood conditions and time course. mRNA are sequenced twice with HiCEP(High-Coverage Expression Profiling) method and clusetered.
The graph of 2nd clustering result is in TranscriptProf.pdf.
File soybean_transcript.zip (1.2 MB)
TranscriptProf.pdf (224 KB)

Data items are the following:
Data itemDescription
Primer HiCEP primer set (5' end - 3' end)
Peak No Peak number of DNA sequences identified by sequencer
2(0) Height min Sample: 2 days after seeding, 0 days after flooding
Minimum peak value in sequencing
2(0) Height max Sample: 2 days after seeding, 0 days after flooding
Maximum peak value in sequencing
2.5(0) Height min Sample: 2.5 days after seeding, 0 days after flooding (control)
Minimum peak value in sequencing
2.5(0) Height max Sample: 2.5 days after seeding, 0 days after flooding (control)
Maximum peak value in sequencing
2.5(0.5) Height min Sample: 2.5 days after seeding, 0.5 days after flooding
Minimum peak value in sequencing
2.5(0.5) Height max Sample: 2.5 days after seeding, 0.5 days after flooding
Maximum peak value in sequencing
3(0) Height min Sample: 3 days after seeding, 0 days after flooding (control)
Minimum peak value in sequencing
3(0) Height max Sample: 3 days after seeding, 0 days after flooding (control)
Maximum peak value in sequencing
3(1) Height min Sample: 3 days after seeding, 1 days after flooding
Minimum peak value in sequencing
3(1) Height max Sample: 3 days after seeding, 1 days after flooding
Maximum peak value in sequencing
3.5(0) Height min Sample: 3.5 days after seeding, 0 days after flooding (control)
Minimum peak value in sequencing
3.5(0) Height max Sample: 3.5 days after seeding, 0 days after flooding (control)
Maximum peak value in sequencing
3.5(1.5) Height min Sample: 3.5 days after seeding, 1.5 days after flooding
Minimum peak value in sequencing
3.5(1.5) Height max Sample: 3.5 days after seeding, 1.5 days after flooding
Maximum peak value in sequencing
4(0) Height min Sample: 4 days after seeding, 0 days after flooding (control)
Minimum peak value in sequencing
4(0) Height max Sample: 4 days after seeding, 0 days after flooding (control)
Maximum peak value in sequencing
4(2) Height min Sample: 4 days after seeding, 2 days after flooding
Minimum peak value in sequencing
4(2) Height max Sample: 4 days after seeding, 2 days after flooding
Maximum peak value in sequencing
Size min Minimum molecular weight of DNA in seuquencing
Size max Maximum molecular weight of DNA in seuquencing
1_Cluster_No Cluseter number of 1st clustering (0-31)
2_Cluster_No Cluseter number of 2nd clustering (1-65)
Target records are filtered in the following conditions:
・Classified in "31" of 1st clutering
・max peak / min peak > 3
3_Peak_No Graph number in "Soybean omics data"
Target records are filtered in the following conditions:
・peak value in treated / peak value in control > 20
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2.7 Soybean metabolites data

Data name Soybean metabolites data
Description of data contents

Metabolites data collected from soybean in different flood conditions and time course, and measured. They are mapped on pathways.
File soybean_metabolites.zip (882 KB)
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2.8 Soybean omics data

Data name Soybean omics data
Description of data contents

The table which is tabulated in metabolome, proteome and transcriptome from experiments and measurements.
File soybean_omics.zip (4.5 MB)
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2.9 References

Data name References
Description of data contents

Experiment protocols and other references
File soybean_description.zip (659 KB)
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2.10 Soybean comparative protein data

Data name Soybean comparative protein data
Description of data contents

Soybean protein data collected from samples in 3 organs (leaf, hypocotyl and root) under 3 stresses (flooding, drought and salt), and separated by two-dimensional polyacrylamide gel electrophoresis.
File soybean_comp_proteomics_list.zip (8 KB)

Data items are the following:
Data itemDescription
Organ Organ of soybean
Stress Stress on soybean
Spot No Spot No on gels
Homologous protein Homologous protein of measured one
Accession No Accession No of homologous protein
Mr(kDa)-theory Theoretical molecular weight of homologous protein
Mr(kDa)-exp Measured molecular weight
pI-theory Protein isoelectric point of homologous protein
pI-exp Measured protein isoelectric point
F.C. Fold change compared with no treatment (without stress) soybean samples
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3. License

Last updated : 2019/11/29

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "SPD©National Agriculture and Food Research Organization (NARO) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Setsuko Komatsu skomatsu[at]fukui-ut[dot]ac[dot]jp

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2019/11/29 Soybean Proteome Database English archive site is opened.
2008/03/05 SPD (http://proteome.dc.affrc.go.jp/Soybean/) is opened.
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5. Literature

Sakata K, Ohyanagi H, Nobori H, Nakamura T, Hashiguchi A, Nanjo Y, Mikami Y, Yunokawa H, Komatsu S
A data resource for plant differential omics.
J Proteome Res, 8:3539-3548.

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6. Contact address

When you have any question about "SPD", contact the following:

Department of Environmental and Food Science,
Fukui University of Technology
Prof. Setsuko Komatsu
E-mail: skomatsu[at]fukui-ut[dot]ac[dot]jp

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