MartView
REGION:
r Limit to (uncheck for entire genome):
Chromosome name; pi From |Base pair   jj |1 f~z\ To|Base pair P3
□ Limit to ENCODE region
Type:
Random Picks
Chr6:108310274-108810273bp *]
Entries in an ENCODE region
s Only C Excluded
' JDisease Genes
Only
Excluded
r Limit to genes with these IDs: (Paste ID list, or upload file)
(NB) AFFY probe IDs should no longer contain the chip name prefix
|AFFY-HG-U133-PLUS-2 ID(s) _*j
Transcripts per gene:
Entries with a 5' UTR
Single r Multiple
p Only C Excluded
Entries with a 3' UTR
s Only r Excluded
GENE ONTOLOGY:
r Evidence code for mapping: Molecular Function
E.g. GO:0008083 or growth factor activity
Biological Process
E.g. GQ:00UB219or cell death
Cellular Component
E.g. 60:0005623 or cell
11 C-by curator |GO:0008Q83
<find> I
EXPRESSION:
r _ .
bio:::;mart Summary
► start
Focus: • Ensembl Genes Species: Homo sapiens
21111 Genes Tola)
► filter
t Disease Genes Only Single
transcript(s) per gene .Has 5' UTR: Only
.Has 3' UTR: Only
53? Genes pass Filters
► output
Wot yet initialised
ff eGenetics/SANBI data
MartShell
^Jc:\WINNT\System32\cmd.exe
MartShell: fin Interactive User Interface to Hart based on Hart Query Language (HQL)
type 'help' for a list of available commands, or type 'help command' to get help for a particular command.
MartShell:. list datasets all;
Ensembl. ensembl_genes_homo_sapiens Ensembl. ensembl_genes_mus_musculus Ensembl. snps_homo_sapiens Ensembl. uega_genes_homo_sapiens HSD.structures Uniprot.proteomes
HartShell> using Ensembl. ensembl_genes_homo_sapiens get xref _swissprot_acc where disease_genes only and nonsynonymous_snps only
?» and transitiembrane_domains only and chromosome_name = 2 as ensembl_set;
HartShell>
MartShell> using Uniprot.proteomes get prot_seq where has splice_uariant only and sprot_list in ensembl set
%
% ;
MEPUPLLLLFSLCShGLULGSEHETRLUhICLFKDVSSUURPUEDHRQUUEUTUGLQLIuLINUDEUNuIUTTNURLKQGDMUDLPRPSCUTLGUPLFSHLCINEQUUDVNLKIiINPDDVGGUKKIHIPSEKIURPDLUL VNNflDGDFAIUKFTKULLQVTGHITlilTPPfllFKSVCEIIUTHFPFDEQNCSHKLGTUTVDGSUUHlNPESDQPDLSNFMESGElilUIKESRGlilKHSUTVSCCPDTPVLDITVHFUHQRLPLVFIUNUIIPCLLFSFLT GLUFVLPTDSGEKMTLSISULLSLTUFLLUIUELIPSTSSflUPLIGKVMLFTMUFUIASIIITUIUINTHHRSPSTHUMPNUURKUFIDTIPNIHFFSTHKRPSREKQDKKIFTEDIDISDISGKPGPPPMGFHSPL IKHPEUKSAIEGIKVIAETMKSDuESNNAAAEUKVUAMUMDHILLGUFMLUCIIGTLAUFAGRLIELNQuG
HALLLUSLLAFLSLGSGCHHRICHCSNRUFLCQESKUTEIPSDLPRNAIELRFULTKLRUIQKGAFSGFGDLEKIEISQNDULEUIEADUFSNLPKLHEIRIEKANNLLVINPEAFQNLPNLQVLLISNTGIKHLPD UHKIHSLQKULLDIQDNINIHTIERNSFUGLSFESUILU1LNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDUFHGASGPUILDISRTRIHSLPSVGLENLKKLRARSTVNLKKLPTLEKLUALHEASLTVPSH CCAFANURRQISELHPICNKSILRCIEUDVHTQTRGQRSSLAEDNESSVSRGFDHTVTEFDVDLCNEJUDUTCSPKPDAFNPCEDIHGVNILRULIUFISILAITGNIIULUILTTSQVKLTUPRFLHCNLAFADLCI GI'r'LLLIASUDIHTKSQ'r'HNVAIDlUQTGAGCDAAGFFTUFASELSUVTLTAITLERUHTITHAHQLDCKUQLRHAASUHUHGUIFAFAAALFPIFGISSVHKUSICLPHDIDSPLSQLVUHSLLULNULAFUUICGC VIHIVLTURNPNIUSSSSDTRIAKRHAHLIFTDFLCHAPISFFAISASLKUPLITUSKAKILLULFHPINSCANPFLVAIFTKNFRRDFFILLSKCGCVEHQAQIVRTETSSTUHNTHPRNGHCSSAPRUTNGSTVI LUPLSHLAQN
MAAAGQLCLLVLSAGLLSRLGAAFNLDTREDNUIRKVGDPGSLFGFSLAHHUIQLQPEDKRLLLUGAPRGEALPLQRANRTGGLVSCDITARGPCTRIEFDNDADPTSESKEDQIUHGUTUQSQGPGGKUUTCAHRVEK RQHUNTKQESRDIFGRCVULSQNLRIEDDHDGGDUISFCDGRLRGHEKFGSCQQGUAATFTKDFHVIUFGAPGTVNUIKGIURUEQKNNTFFDMNIFEDGPVEUGGETEHDESLUPUPANSVLGLLFLTSUSVTDPDQF UVKTRPPREQPDTFPDUMHNSVLGFSLDSGKGIUSKDEITFUSGAPRANHSGAUULLKRDHKSAHLLPEHIFDGEGLASSFGVDUAUUDLNKDGUQDIUIGAPQVFDRDGEUGGAUVUVMNQQGRUINNUKPIRLNGT HDSHFGIAUKNIGDINQDGVPDIAUGAPVDDLGKUFIVHGSANGINTKPTQULKGISPVFGVSIAGNMDLDRNSVPDUAUGSLSDSUTIFRSRPUINIQKTITUTPNRIDLRQKTACGAPSGICLQUKSCFEVTANP AGVNPSISIUGTLEAEKERRKSGLSSRUQFRNQGSEPKVTQELTLKRQKQKUCHEETLUILQDNIRDKLRPIPITASUEIQEPSSRRRUNSLPEULPILNSDEPKTAHIDUHFLKEGCGDDNUCNSNLKLEVKFCTRE GNQDKFSVLPIGKGUPELULKDGKDIALEITUTNSPSNPRNPTKDGDDAHEAKLIATFPDTLTVSAVRELRAFPEKQLSCUANQNGSQADCELGNPFKRNSNUTFVLULSTTEUTFDTPDLDINLKLETTSNQDNLA PITAKAKUUIELLLSUSGUAKPSQUVFGGTUUGEQAHKSEDEUGSLIEVEFRUINLGKPLTNLGTATLNIQUIPKEISNGKlilLLVLUKUESKGLEKUTCEPQKEINSLNLTESHNSRKKREITEKQIDDNRKFSLFAE RKVQTLNCSUNUNCUNIRCPLRGLDSKASLILRSRLUlNSTFLEEVSKLNVLDILHRAFIDUTAAAENIRLPNAGTQURUTUFPSKTUAQVSGUPUlilIILUAILAGILHLALLUFILlilKCGFFKRSRVDDSUPRVHAU RIRKEEREIKDEKYIDNLEKKQWITKWNRNESYS
HKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCUPDGALRCPGPTAGLTRLSLAVLPUKUIPSQAFRGLNEUIKIEISQIDSLERIEANAFDNLLNLSEILIQNTKNLRVIEPGAFINLPRLK'r'LSICNTGIRK FPDUTKUFSSESNFILEICDNLHITTIPGNAFQGHNNESUTLKLVGNGFEEUQSHAFNGTTLTSLELKENUHLEKHHNGAFRGATGPKTLDISSTKLQALPSVGLESIQRLIATSSVSLKKLPSRETFUNLLEATLT VPSHCCAFRNLPTKEQNFSHSISENFSKQCESTURKUSNKTLVSSHLAESELSGWDVEVGFCLPKTPRCAPEPDAFNPCEDIHGVDFLRULIULINILAIHGNHTULFULLTSRVKLTUPRFLHCNLSFADFCHGLV LLLIASUDSQTKGQVVNHAIDlilQTGSGCSTAGFFTUFASELSUVTLTUITLERlilHTITVAIHLDQKLRLRHAILIHLGGlilLFSSLIAHLPLUGUSNVHKUSICFPHDUETTLSQU'r'ILTILILNUUAFFIICACVIK IVFAURNPELHATNKDTKIAKKHAILIFTDFTCHAPISFFAISAAFKUPLITUTNSKULLULFVPINSCANPFLVAIFTKTFQRDFFLLLSKFGCCKRRAELVRRKDFSAVTSNCKNGFTGSNKPSQSTLKLSTLHC QGTALLDKTRVTEC
MALLIHLKTUSELRGRGDRIAKUTFRGQSFVSRULENCEDUADFDETFRUIPUASSIDRNEHLEIQUFNVSKUFSNKLIGTFRMULQKUUEESHUEUTDTLIDDNNAIIKTSLCUEURVQATDGTUGSlilDDGDFLGDE SLQEEEKDSQETDGLLPGSRPSSRPPGEKSFRRAGRSUFSAMKLGKNRSHKEEPQRPDEPAULEHEDLDHLAIRLGDGLDPDSUSLASUTALTTNUSNKRSKPDIKMEPSAGRPHDVQUSITUIEARQLUGLNHDPU UCUEUGDDKKVTSMKESTNCPVVNEVFUFDFHUSPDUMFDKIIKISUIHSKNLLRSGTLUGSFKHDUGTUVSQPEHQFHHKUAILSDPDDISSGLKGVUKCDUAUUGKGDNIKTPHKANETDEDDIEGNLLLPEGUP PERQUARFVUKIVRAEGLPRHNTSLHANUKKAFIGENKDLUDPVUQUFFAGQKGKTSUQKSSVEPLI1INEQUUFTDLFPPLCKRHKUQIRDSDKUNDUAIGTHFIDLRKISNDGDKGFLPTLGPAI1IUNHVGSTRNVTL LDEHQDLNEGLGEGUSFRARLLLGLAUEIUDTSNPELTSSTEUQUEQATPISESCAGKHEEFFLFGAFLEASMIDRRNGDKPITFEUTIGNVGNEUDGLSRPQRPRPRKEPGDEEEUDLIQNASDDEAGDAGDLASU
I |jj|Microsc.ftPo... | 63bin
Key abstractions of generic system
Mart
GENE CENTRAL
gene_id(PK)
gene_stable_id
gene_start
gene_chrom_end
chromosome
gene_display_id
description
Dataset
Attribute
Filter
BioMart - a distributed architecture
XML
XML
MartShell examples
MartShell> using MSD.msd get pdb_id where resolution_less < 1.5 and has_ec_info only;
1931 1941 larb ...
MartShell> using MSD.msd get pdb_id where resolution_less < 1.5 and has_ec_info only as q;
MartShell> using
Ensembl.hsapiens_gene_ensembl get sequence transcript_flanks+1000 where pdb in q;
ENST00 000270142.2      ENSG000 00142168.2
strand=forward     chr=21 assembly=NCBI34 downstream flanking sequence of transcript
only
AAACTAAATTAGCTCTGATACTTATTTATATAAACAGCTTCAGTGGAA
MartShell examples (cont)
MartShell> using Ensembl.hsapiens_gene_ensembl
get gene_stable_id, hugo, go_description
where chr_name = 3 and
3.band_start = q22.1 and
3.band_end = q22.3 and est.anatomical_site = retina;
ENSG00000051382 PIK3CB phosphoinositide 3-kinase complex
ENSG00000163914 RHOG-protein coupled photoreceptor activity ...