Difference between revisions of "QLanners Week 14"

Revision as of 00:05, 1 December 2017

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:

• Gene ID from each database
• Description/Function (ensembl)
• DNA Sequence (ensembl)
• Protein Sequence (UniProt)
• Locus tag (NCBI)
• Also Known As (NCBI)
• Consensus Sequence (JASPAR)
• Regulation (SGD)
• Interaction (SGD)
• Similar Proteins (UniProt)
• Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:

• Gene ID (this will be the matrix id
• Sequence Logo
• Frequency Matrix
• also get class and family

Breakdown of what we want from all other databases:
NCBI:

• Gene ID
• Locus Tag
• Also Known As
• Also get RefSeq IDs for chromosome, mRNA, and protein.

Ensembl:

• Gene ID
• Description/Function
• DNA Sequence
• also get chromosomal location, about this gene

UniProt:

• Gene ID: P10961 (HSF_YEAST)
• Protein Sequence
  • MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI

INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK

• Similar Protein: N1P1W2 and ID of Similar Protein: P10961
• Protein Type/Name: Heat shock factor protein
• Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

SGD:

• Gene ID
  • Standard Name HSF1
  • Systematic Name YGL073W
  • SGD ID S000003041
• Regulation
  • Regulators: 6
  • Targets: 478
• Interaction
  • Total Interactions: 85 total interactions for 71 unique genes
  • Physical Interactions:
    • Affinity Capture-MS: 11
    • Affinity Capture-RNA: 1
    • Affinity Capture-Western: 4
    • Biochemical Activity: 11
    • Co-localization: 3
    • Reconstituted Complex: 2
    • Two-hybrid: 3
  • Genetic Interactions:
    • Dosage Rescue: 16
    • Negative Genetic: 8
    • Phenotypic Enhancement: 1
    • Phenotypic Suppression: 5
    • Synthetic Growth Defect: 2
    • Synthetic Haploinsufficiency: 1
    • Synthetic Lethality: 6
    • Synthetic Rescue: 11
• Gene Ontology
  • Summary: Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling
  • Molecular Function:
    • Manually Curated: DNA binding transcription factor activity (IDA)
    • High-Throughput: sequence-specific DNA binding (HDA)
  • Biological Process
    • Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)
  • Cellular Component:
    • Manually Curated: nucleus (IDA)
    • High-Throughput: mitochondrion (HDA)