Ebachour: /* Electronic Journal */ Added Electronic Journal

2017-12-05T07:46:59Z

‎Electronic Journal: Added Electronic Journal

Ebachour: Added logistics that you require

2017-12-05T07:41:11Z

Added logistics that you require

Ebachour: Started Week 14

2017-12-05T07:30:05Z

Started Week 14

New page

===Fields to Pull From Each Database===
''' EVERYTHING IN THIS SECTION WAS PULLED FROM QUINN'S JOURNAL PAGE '''

We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*Description/Function ''Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*Gene Map 
[[File:Saccharomycescerevisiae HSF1.pdf]]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*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)''

← Older revision		Revision as of 07:46, 5 December 2017
Line 1:		Line 1:
	=Electronic Journal=		=Electronic Journal=
		+	* Simon and worked a lot in class and cracked the code on how to access the JASPAR data relevant using an gene id
		+	* We ran into complication that we think are due to CORS
		+	* We decided that our branch shouldn't really be separate from the gene-database-apis branch, so we decided to merge the two for the sake of ease
		+	** This means that there are now four people working on our branch
		+	* I also did some work on my own, trying to figure out if there was an easy fix for the CORS issue
		+	* I found a local fix which uses a chrome extension to trick (sort of) Jaspar somehow, I'm not sure that I really understand how it works, but it does
		+	* I committed all this code, which works on my own machine, but I still need to confirm with Dondi how this would work for GRNsight.
		+	* I also created the master object that would contain all of the data that we need from all the sources

	=Fields to Pull From Each Database=		=Fields to Pull From Each Database=

@@ Line 1: / Line 1: @@
-===Fields to Pull From Each Database===
+=Electronic Journal=
 ''' EVERYTHING IN THIS SECTION WAS PULLED FROM QUINN'S JOURNAL PAGE '''
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 ***''Manually Curated: nucleus (IDA)''
 ***''High-Throughput: mitochondrion (HDA)''

Ebachour Week 14 - Revision history

Ebachour: /* Electronic Journal */ Added Electronic Journal

Ebachour: Added logistics that you require

Ebachour: Started Week 14