※ Supplementary materials:
Supplementary materials for our SSP articles:

1. The statistics significant GO terms/groups in our results. You can download the .xls file here.

There are four sub-tables in the SUMO_GO.xls file:

    GO_table1: In this table, we list the top 25 over-representated (The Enrichment_ratio > 1) GO terms/groups with the p-value < 0.0001, which are over-represented in the SUMO substrates against whole human proteome.

    GO_table2: We list the 59 GO terms/groups which the p-value < 0.0001, which GO terms/groups are over-representated (The Enrichment_ratio > 1) in SUMO substrates against whole human proteome. We mark the GO terms in three color: component in yellow, function in red, and process in blue. Please check the AMIGO for the detailed definition of GO.

    GO_table3: In this table, we list the 95 GO terms/groups which the p-value < 0.0001. The under-represented GO groups are marked in blue.

    GO_table4: In this table, we list the 375 GO terms/groups which the p-value < 0.05, briefly.

2. The statistics significant Interpro terms/protein domains in our results. You can download the .xls file here.

There are three sub-tables in the SUMO_IPR.xls file:

    IPR_table1: In this table, we list the 69 protein domains which the p-value < 0.0001, which are over-representated (The Enrichment_ratio > 1) in SUMO substrates against whole human proteome.

    IPR_table2: In this table, we list the 87 protein domains which the p-value < 0.0001. And the under-represented protein domains are marked in blue.

    IPR_table3: In this table, we list the 422 protein domains which the p-value < 0.05, briefly.

3. The hypergeometric distribution script was written in perl. You can get it here. Also, we ackowledge Xing Yi (UCLA) to provide the equation and python code. You can mail to him to get the Python code version of this program.

4. Total statistics analysis for GO terms/groups and Interpro/protein domains. There are 4,444 GO iterms and 4,811 protein domains with their Enrichment_ratio and p-value. You can use it for your own analysis. Please download the GO list or Interpro list.

5. We downloaded the GO (08/10/2004) and Interpro (23/06/2004) association files from EBI and searched for the GO and Interpro annotations of human proteins.

There are 4,444 GO terms are used for whole human proteome annotation in file hsALL2GO, with the names of GO terms and their number. And there are 1,318 GO terms are represented in SUMO substrates (SS2GO).

There are 4,811 Interpro terms are used for whole human proteome annotation in file hsALL2IPR, with the names of Interpro terms and their number. And there are 1,417 Interpro terms are represented in SUMO substrates (SS2IPR).

6. We mapped the SUMO substrates and whole human proteome to GO and Interpro, from EBI, respectively.

Totally 24,090 proteins of whole human proteome were annotated by GO, while 1,956 SUMO substrates were annotated.

Totally 26,873 proteins of whole human proteome were annotated by Interpro, while 2,264 SUMO substrates were annotated.



CITATION:
If you use our SSP v1.0 or data for your research, please cite the following article:

Fengfeng Zhou, Yu Xue, Hualei Lu, Guoliang Chen, Xuebiao Yao. A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus. FEBS Lett. 2005 Jun 20;579(16):3369-75. Supplementary materials.

A total dataset of 2,683 potential SUMO substrates in human and mouse identified is freely assessable in txt or pdf format.


Last update: Jun. 19th, 2005
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