H-InvDB_9.0 released on May 27, 2015. Search by Keyword H-Inv ID (HIT) H-Inv cluster ID (HIX) H-Inv protein ID (HIP) H-Inv gene family/group (HIF) Accession number Chromosome number Chromosome band Definition* Data source ID --- CCDS ID dbSNP ID (rs number) EC number Ensembl ID EntrezGene ID FR ID FR Accession number GO ID GO name* HGNC gene symbol HGNC gene name* InterPro ID InterPro name* OMIM ID OMIM title* Pathway ID Pathway name* RefSeq (gene) ID RefSeq (protein) ID SCOP ID UniProt for Advanced Search

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Current dataset

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Previous dataset

H-InvDB_9.0 released on May 27, 2015. (Erratum released on June 18, 2015.)
	List of H-Invitational IDs

acc2hinv_id.txt.gz	2.7M	Text File
Format 1: DNA databank accession numbers, 2: HIT : H-Invitational transcript, 3: HIX : H-Invitational clusters, 4: cDNA data provider

List of new, deleted and updated H-Invitational IDs

new_del_update_hinvid.txt

720K

Text File

Annotation data sets

H-InvDB-HIX_9.0 2015. 6
SET of all H-Inv clusters (Flat File)	43M	Flat File
SET of all H-Inv clusters (XML)	56M	XML File
Annotation for all H-Inv clusters are provided in both flat file and XML format
H-InvDB-HIT_9.0 2015. 6
SET of all H-Inv transcripts(Flat File)	614M	Flat File
SET 1 of all H-Inv transcripts (XML)	197M	XML File
SET 2 of all H-Inv transcripts (XML)	189M	XML File
SET 3 of all H-Inv transcripts (XML)	180M	XML File
SET 4 of all H-Inv transcripts (XML)	105M	XML File
SET 5 of all H-Inv transcripts (XML)	59M	XML File
NOTES: Annotation for all H-Inv transcripts are provided in both flat file and XML format
H-InvDB-HIP_9.0 2015. 6
SET of all H-Inv proteins (Flat File)	413M	Flat File
SET 1 of all H-Inv proteins (XML)	165M	XML File
SET 2 of all H-Inv proteins (XML)	158M	XML File
SET 3 of all H-Inv proteins (XML)	116M	XML File
NOTES: Annotation for all H-Inv proteins are provided in both flat file and XML format

Section data of annotation

H-InvDB-HIX-Annotation_9.0 2015. 6
SET of all H-Inv clusters (Flat File)	35M	Flat File
Section of basic annotation for H-Inv clusters are provided flat file format
H-InvDB-HIT-Annotation_9.0 2015. 6
SET of all H-Inv transcripts (Flat File)	436M	Flat File
NOTES: Section of basic annotation for H-Inv transcripts are provided flat file format.
H-InvDB-Expression_8.1
SET of H-Inv clusters (Flat File)	7.9M	Flat File
Section of tissue-specific expression data is provided flat file format.
H-InvDB-DiseaseInfo_8.0
SET of H-Inv clusters (Flat File)	7.5M	Flat File
Section of disease information is provided flat file format.
H-InvDB-Evolution_7.1
SET of all H-Inv transcripts (Flat File)	24M	Flat File
Section of molecular evolutionary analysis is provided flat file format.
H-InvDB-3Dstructure_8.0
SET of all H-Inv transcripts (Flat File)	29M	Flat File
NOTES: Section of prediction of 3-D structure of H-Inv transcripts by GTOP (http://sybock.genes.nig.ac.jp/~hinv3/gtop.html) are provided flat file format
H-InvDB-Subcellular_9.0 2015. 6
SET of all H-Inv transcripts (Flat File)	18M	Flat File
NOTES: Section of prediction of subcellular localization by WoLF PSORT, TargetP, TMHMM and SOSUI are provided flat file form

Sequence data sets

Nucleotide data sets 2015. 6
All H-Invitational transcripts (HITs)	124M	Flat File
Representative H-Invitational transcripts (HITs)	31M	Flat File
Representative alternative variants (RASV) of H-Invitational transcripts (HITs)	46M	Flat File
H-Inv2 full-length cDNA dataset (HITs)	47M	Flat File
H-Invitational cluster genome sequence (HIXs)	644M	Flat File
NOTES: 1) Nucleotide sequences of all H-Inv transcripts (HITs) in FASTA format. 2) Nucleotide sequences of representative H-Inv transcripts (HITs) in FASTA format. 3) Nucleotide sequences of representative splicing variants (RASV) of H-Inv transcripts (HITs) in FASTA format. 4) Nucleotide sequences of all H-Inv cDNAs (HITs) in FASTA format. 5) Nucleotide sequences of the genome for the all H-Inv clusters (HIXs) in FASTA format. Headline> HIT version | HIX version | HIP version | DNA databank accession number | "FS": frame shift error if revised or "NO" for no revision | "IM": remaining intronic sequence if revised or "NO" for no revision | "HC": function if human curated or "AA" for auto-annotated| Frame (+3 to -3) | Position of CDS (start..end) | Definition Body: cDNA sequences
Amino acid data sets 2015. 6
All H-Invitational trsnscripts (HITs)	47M	Flat File
Representative H-Inv transcripts (HITs)	9.7M	Flat File
Representative alternative variants (RASV) of H-Inv transcripts (HITs)	18M	Flat File
H-Inv2 full-length cDNA dataset (HITs)	14M	Flat File
All H-Invitational proteins (HIPs)	37M	Flat File
1) Translation of all H-Inv transcripts (HITs) in FASTA format. 2) Translation of representative H-Inv transcripts (HITs) in FASTA format. 3) Translation of representative alternative variants (RASV) of H-Inv transcripts (HITs) in FASTA format. 4) Translation of all H-Inv cDNAs (HITs) in FASTA format. 5) Translation of all H-Inv proteins (HIPs) in FASTA format. Headline> HIT version | HIX version | HIP version | DNA databank accession number | "FS": frame shift error if revised or "NO" for no revision | "IM": remaining intronic sequence if revised or "NO" for no revision | "HC": function if human curated or "AA" for auto-annotated| Frame (+3 to -3) | Position of CDS (start..end) | Definition Body: translation

Results of computational analysis  New! (revised)

Multiple alignment information 2015. 5
SET of all MULTIPLE ALIGNMENT(Flat File)	347M	Flat File
NOTES: "FMULTI" provides multiple-alignments of all the H-Inv transcripts and RefSeq sequences mapped in the same H-Inv cluster(HIX), against human genome sequence.
Positional information of mapping 2015. 6
Data of all positional information for all the exon(Flat File)	124M	Flat File
NOTES: "FMULTIP"; FMULTIP.tar.gz (mALNp/.tbl) provides positional information for all the exon of all the H-Inv transcripts and RefSeq sequences mapped in the same H-Inv cluster(HIX), against human genome sequence. Format: 01:HIT (or acc), 02:HIX (or temporally cluster-id), 03:key (=acc_chr_sno), 04:seq1 ("genome"), 05:seq2 (cDNA_acc), 06:strand, 07:exon_no, 08:type[N:not aligned part of seq1(genome); U:unmapped part of seq2(cDNA); A:alignment, D:deletion, I:insertion; G:gap due to other member)], 09:start_seq1 (genome), 10:end_seq1 (genome), 11:start_seq2 (cDNA), 12:end_seq2 (cDNA) (or gap_length if 08:type='G')
The positional information of the exon, CDS and UTR for representative H-Inv transcripts (HITs) in GFF3 format.	7.6M	GFF3 File
The positional information of the exon, CDS and UTR for all H-Inv transcripts (HITs) in GFF3 format.	25M	GFF3 File
NOTES: "h-inv_pub_rep.gff3.gz","h-inv_pub.gff3.gz"; The positional information of the exon, CDS and UTR in GFF3 format. Format:01: "seqid (HIT)", 02: "source", 03: "type", 04: "start", 05: "end", 06: "score", 07: "strand", 08: "phase", 09: "attributes" Attributes (exon):ID=HIX, Name=HIT, Note=HUGO gene symbol Attributes (CDS):ID=HIT, Parent=HIX, Name=HIT, Alias=definition, Note=HUGO gene symbol, accession Attributes (UTR):Parent=HIT, Name=HIT
H-ANGEL matrix
Gene expression matrix of H-ANGEL (Flat File)	25M	Flat File
NOTES: "H-ANGEL_matrix.txt.gz" provides gene expression matrix of H-ANGEL. The followings are the No. of column and each description. Format: 1: Type of platform, 2: experimental ID added by each provider, 3: primer/probe ID. e.g. GeneChip Identifier, 4: 10 categories collapsed by the avarage of 40 categories, 5: 10 categories collapsed by the maximum value of 40 categories, 6: 40 categories, 7: Acc corresponding to the primer/probe, 8: start site of the primer/probe on the genome, 9: end site of the primer/probe on the genome, 10: Absolute value of the expression data for EST and SAGE only, NaN otherwise, 11: HIX, 12: UniGene ID, 13: start site of HIX on the genome, 14: end site of HIX on the genome, 15: strand of the locus, 16: Acc(s) included within HIX.
Molecular evolutionary annotation (Evola)
SET of Evola ortholog list		Flat File
"Evola.txt.gz": provides ortholog accession number list of Evola
Inter-species multi-FASTA (Transcript)
SET of Evola ortholog sequences (Transcript)		Flat File
NOTES: "NFAS.tar.gz" provides multiple FASTA of transcript nucleotide sequences of human and other species orthologs.
Inter-species multi-FASTA (Protein)
SET of Evola ortholog sequences (Protein)		Flat File
NOTES: "PFAS.tar.gz" provides multiple FASTA of protein amino acid sequences of human and other species orthologs.
Phylogenetic trees
SET of Evola duplicate gene family trees (Flat File)		Flat File
NOTES: "NJ.tar.gz" provides the phylogenetic trees (phb files) constructed by the Neighbor-joining method (amino acid)
Human protein complex database with quality index (PCDq), data set New! 2015. 11
Protein complex list, their subunits (members), and related annotation.	1.5M	TSV Files (tar.gz file)
NOTES: "complexList.tsv" provides complex ID, name, etc.   "subunitMembers.tsv" provides subunits (members) of each complex and related annotations.   "public_ppi.tsv" provides PPI data used for complex prediction. File format is described in README file included in download package.
A subset of H-InvDB annotation data sets with supporting proteome evidence   2015. 7
SET of H-Inv clusters with supporting proteome evidence (Flat File)	25M	Flat File
SET of H-Inv clusters with supporting proteome evidence (XML)	33M	XML
SET of H-Inv transcripts with supporting proteome evidence (Flat File)	146M	Flat File
SET of H-Inv transcripts with supporting proteome evidence (XML)	178M	XML
SET of H-Inv proteins with supporting proteome evidence (Flat File)	57M	Flat File
SET of H-Inv proteins with supporting proteome evidence (XML)	61M	XML
NOTES: Subsets of H-InvDB loci, transcripts, and proteins, with supporting evidences of expression confirmed in comprehensive proteomic experiments. Those classified as "protein level" or "transcript level" expression in C-HPP are included.
Transcripts and clusters unmapped to human genome   2015. 5
Clusters of transcripts unmapped to human genome (Flat File)	2.7M	Flat File
Clusters of transcripts unmapped to human genome (XML)	3.0M	XML
Transcripts unmapped to human genome (Flat File)	14M	Flat File
Transcripts unmapped to human genome (XML)	15M	XML
NOTES: Data set of transcripts (HIT) and clusters (HIX) that are not mapped to human genome.