HEAT HELP

HELP

H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. This technique is called gene set enrichment analysis (GSEA), and is popularly used in analyzing results of microarray experiments. Fisher's exact probability is used in statistical tests of HEAT.

1. Usage

(1) Gene-Set Submission

Submit two or more human gene IDs. Acceptable IDs are HUGO Gene Symbols, Accession Numbers of INSD (DDBJ/EMBL/GenBank), H-InvDB Transcript IDs (HIT), Locus IDs (HIX), Protein IDs (HIP), UniProt Accession Numbers, RefSeq, GeneID, PDB ID, Ensembl Transcript IDs, Ensembl Gene IDs, FLJ IDs, Clone IDs, KEGG IDs, and HPRD IDs. IDs need to be separated by spaces or commas. You can insert return codes. You can upload a text file with gene IDs. By pushing the Submit Gene-Set button, the HEAT converts given IDs into H-InvDB representative transcript IDs. Here, the HEAT system utilizes the web service of ID Converter System to convert human gene IDs.

(2) Execution

The submitted gene IDs are converted into corresponding Transcript IDs (HIT) of H-InvDB representative transcripts, and are shown. If there are no corresponding IDs in H-InvDB, the IDs are left blank, and will not be used in the enrichment analysis. Push the Execute button to start finding enriched features for this gene set.

(3) Results

Enriched features of the given gene set is shown. For each feature, the ID and name of feature, the number of occurrences/genes of a submitted gene set, the number of occurrences/genes among all H-InvDB representative transcripts, and P-values are shown. The features with P-values smaller than 0.01, sorted by P-values, are shown. The following features of H-InvDB are analyzed.

AnnotationNumber
InterPro7,532
Gene Ontology: Biological Process638
Gene Ontology: Cellular Component197
Gene Ontology: Molecular Function978
KEGG pathway175
Chromosomal band881
Gene family3,631
SCOP (Structural domains)2,655
Subcellular localization prediction (by using Wolf PSORT)11
Tissue-specific gene expression (10 tissue categories defined in H-ANGEL)10
Sequence motifs in promoter regions (JASPAR)130
Protein-Protein Interaction (PPI)10,869

If you click the "download" button, you can download the results in text format. If you click the number of occurrences in the feature list, HITs containing the corresponding feature will be shown in pop-up windows.

(4) Statistical Test

HEAT conducts gene set enrichment analysis by calculating P-values using Fisher's exact probability test. Let N be the number of all protein-coding representative transcripts in H-InvDB, n be the number of occurrences of a particular feature, K be the number of genes submitted, and k be the number of occurrences of the feature in the given gene set. Then, the P-value is calculated by the following equation.
P-value

2. References

The HEAT system is introduced in the following paper. Please cite this paper if you find it useful.

Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, Imanishi T, and Gojobori T (2009) H-InvDB in 2009, extended database and data mining resources for human genes and transcripts. Nucleic Acids Research 38 (Database Issue): D626-D632.

- Other related papers

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, and Sugano S (2004) Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology 2: 856-875.

Genome Information Integration Project and H-Invitational 2* (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research 36 (Database Issue): D793-D799.
*Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori T.

Imanishi T and Nakaoka H (2009) Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Research 37 (Web Server Issue) gkp355.

3. Inquiries

Please send questions about the HEAT system to the H-InvDB help-desk by emails.

4. Links to Related Sites

5. Release History

  • April 8, 2009 Official public release of the HEAT system.
  • April 22, 2009 Release of H-Inv gene family/group (HIF) viewer.
  • May 29, 2009 A paper about ID Converter System was added in the Reference.
  • July 24, 2009 Update of H-Inv gene family/group (HIF) viewer data (HIF62).
  • October 29, 2009 A paper about HEAT was added in the Reference.
  • January 13, 2010 Promoter motifs of JASPAR are added. Design of HEAT was revised.
  • June 28, 2011 PPI information was added. This annotation data was obtained from PPI View, a sub-database of H-InvDB.