H-InvDB_8.3 released on March 26, 2013. 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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H-InvDB_8.3 released on March 26, 2013.
	List of H-Invitational IDs

acc2hinv_id.txt.gz	3.0M	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

256K

Text File

Annotation data sets

H-InvDB-HIX_8.1
SET of all H-Inv clusters (Flat File)	52M	Flat File
SET of all H-Inv clusters (XML)	68M	XML File
Annotation for all H-Inv clusters are provided in both flat file and XML format
H-InvDB-HIT_8.2
SET of all H-Inv transcripts(Flat File)	555M	Flat File
SET 1 of all H-Inv transcripts (XML)	148M	XML File
SET 2 of all H-Inv transcripts (XML)	138M	XML File
SET 3 of all H-Inv transcripts (XML)	141M	XML File
SET 4 of all H-Inv transcripts (XML)	135M	XML File
SET 5 of all H-Inv transcripts (XML)	82M	XML File
NOTES: Annotation for all H-Inv transcripts are provided in both flat file and XML format
H-InvDB-HIP_8.1
SET of all H-Inv proteins (Flat File)	311M	Flat File
SET 1 of all H-Inv proteins (XML)	106M	XML File
SET 2 of all H-Inv proteins (XML)	105M	XML File
SET 3 of all H-Inv proteins (XML)	112M	XML File
SET 4 of all H-Inv proteins (XML)	3.7M	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_8.1
SET of all H-Inv clusters (Flat File)	42M	Flat File
Section of basic annotation for H-Inv clusters are provided flat file format
H-InvDB-HIT-Annotation_8.2
SET of all H-Inv transcripts (Flat File)	387M	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)	8.8M	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_8.0
SET of all H-Inv transcripts (Flat File)	19M	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
All H-Invitational transcripts (HITs)	138M	Flat File
Representative H-Invitational transcripts (HITs)	27M	Flat File
Representative alternative variants (RASV) of H-Invitational transcripts (HITs)	46M	Flat File
H-Inv2 full-length cDNA dataset (HITs)	45M	Flat File
H-Invitational cluster genome sequence (HIXs)	501M	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
All H-Invitational trsnscripts (HITs)	55M	Flat File
Representative H-Inv transcripts (HITs)	8.9M	Flat File
Representative alternative variants (RASV) of H-Inv transcripts (HITs)	19M	Flat File
H-Inv2 full-length cDNA dataset (HITs)	14M	Flat File
All H-Invitational proteins (HIPs)	54M	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

Multiple alignment information
SET of all MULTIPLE ALIGNMENT(Flat File)	312M	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
Data of all positional information for all the exon(Flat File)	95M	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.	6.7M	GFF3 File
The positional information of the exon, CDS and UTR for all H-Inv transcripts (HITs) in GFF3 format.	28M	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
Protein complex list, their subunits (members), and related annotation.	6.5M	TSV Files (tar.gz file)