GcatWiki - User contributions [en]

JP Apr 12 16

2016-04-12T18:45:15Z

Jupreziosi:

[[Julia Preziosi]]

"There's a genome's worth of stories to tell" - Dr. C

-emphasize that 30 mins post feeding - feeding starts at swallow

--don't even let the snake eat = next experiment

JP Apr 12 16

2016-04-12T18:43:46Z

Jupreziosi:

[[Julia Preziosi]]

"There's a genome's worth of stories to tell" - Dr. C

-emphasize that 30 mins post feeding - feeding starts at swallow

JP Apr 12 16

2016-04-12T18:43:01Z

Jupreziosi:

[[Julia Preziosi]]

"There's a genome's worth of stories to tell" - Dr. C

JP Apr 12 16

2016-04-12T18:42:55Z

Jupreziosi: Created page with "Julia Preziosi "There's a genome's worth of stories to tell" - Dr.C"

[[Julia Preziosi]]

"There's a genome's worth of stories to tell" - Dr.C

Julia Preziosi

2016-04-12T18:42:30Z

Jupreziosi:

[[Group 2 intestines]]

[[JP Resources]]

Notes, Spring 2016

[[JP Jan 12 16]]

[[JP Jan 14 16]]

[[JP Jan 19 16]]

[[JP Jan 21 16]]

[[JP Jan 26 16]]

[[JP Jan 28 16]]

[[JP Feb 02 16]]

[[JP Feb 04 16]]

[[JP Feb 09 16]]

[[JP Feb 11 16]]

[[JP Feb 16 16]]

[[JP Feb 18 16]]

[[JP Feb 23 16]]

[[JP Feb 25 16]]

[[JP Mar 08 16]]

[[JP Mar 10 16]]

[[JP Mar 17 16]]

[[JP Mar 22 16]]

[[JP Mar 24 16]]

[[JP Apr 05 16]]

[[JP Apr 07 16]]

[[JP Apr 12 16]]

JP Apr 07 16

2016-04-07T18:53:37Z

Jupreziosi:

[[Julia Preziosi]]

Last day to figure out our story before oral presentation.

Found a cool gene. - Possible OFF response being queued up at start of feeding.

Contig887_EIF4EBP1_Eukaryotic_translation_initiation_factor_4E-binding_protein_1_Bos_taurus

upregulated

Codes for 4EBP1 protein which binds to eIF4E and inhibits it

eIF4E is an initiation of translation limiting factor

4EBP1 are negative regulators of cell growth by acting on the translational process of the cell

Can be unbound by insulin signaling -> cell growth

-phosphorylation = no interaction = cell growth

Insulin phosphorylates => cell growth

Insulin is raised during feeding. Falls after feeding.

--maybe the signal begins with the feeding process, and is preparing for an “off” signal (lowered insulin -> binding -> stop growth)

JP Apr 07 16

2016-04-07T18:28:53Z

Jupreziosi:

[[Julia Preziosi]]

Last day to figure out our story before oral presentation.

Found a cool gene.

Contig887_EIF4EBP1_Eukaryotic_translation_initiation_factor_4E-binding_protein_1_Bos_taurus

upregulated

Codes for 4EBP1 protein which binds to eIF4E and inhibits it

eIF4E is an initiation of translation limiting factor

4EBP1 are negative regulators of cell growth by acting on the translational process of the cell

Can be unbound by insulin signaling -> cell growth

-phosphorylation = no interaction = cell growth

Insulin phosphorylates => cell growth

Insulin is raised during feeding. Falls after feeding.

--maybe the signal begins with the feeding process, and is preparing for an “off” signal (lowered insulin -> binding -> stop growth)

JP Apr 07 16

2016-04-07T17:36:37Z

Jupreziosi: Created page with "Julia Preziosi Last day to figure out our story before oral presentation."

[[Julia Preziosi]]

Last day to figure out our story before oral presentation.

Julia Preziosi

2016-04-07T17:35:22Z

Jupreziosi:

JP Apr 05 16

2016-04-05T18:56:17Z

Jupreziosi:

Julia Preziosi

Saw the snakes eat today. Start timing the snakes right when the mouse's tail goes into the mouth (one final swallow). Then 30 minutes after we euthanize. The snakes feed head - tail usually.

was absent last thursday. Teammates looked for pathways.

We now have 14 genes, after looking at the genes' pathways and involvement. We ruled out passenger genes (metabolism, cell growth, DNA transcription), and focused on genes in signaling pathways.

Of these, I think 7 look promising for their roles in regulation and signaling.

Contig887_EIF4EBP1_Eukaryotic_translation_initiation_factor_4E-binding_protein_1_Bos_taurus

Contig6877_Protein_of_unknown_function_1064 [Contig6877_ERH_enhancer_of_rudimentary_homolog]

Contig5647_Mfap2_Microfibrillar-associated_protein_2_Mus_musculus

Contig5342_IMPDH1_Inosine-5_prime-monophosphate_dehydrogenase_1_Homo_sapiens

Contig4903_Protein_of_unknown_function_897 [Contig4903_zinc_finger_with_KRAB_and_SCAN_domains_7-like_isoform_X3]

Contig2831_CABLES1_CDK5_and_ABL1_enzyme_substrate_1_Homo_sapiens

Contig1116_MCM5_DNA_replication_licensing_factor_MCM5_Homo_sapiens

JP Apr 05 16

2016-04-05T18:55:26Z

Jupreziosi:

JP Apr 05 16

2016-04-05T18:45:19Z

Jupreziosi:

JP Apr 05 16

2016-04-05T18:37:40Z

Jupreziosi: Created page with "Julia Preziosi Saw the snakes eat today. Euthanize the snakes right when the mouse's tail goes into the mouth (one final swallow). The snakes feed head - tail usually. was ..."

Julia Preziosi

Saw the snakes eat today. Euthanize the snakes right when the mouse's tail goes into the mouth (one final swallow). The snakes feed head - tail usually.

was absent last thursday. Teammates looked for pathways.

We now have 14 genes, after looking at the genes' pathways and involvement. We ruled out passenger genes (metabolism, cell growth, DNA transcription), and focused on genes in signaling pathways.

Julia Preziosi

2016-04-05T18:10:02Z

Jupreziosi:

JP Mar 24 16

2016-03-24T18:48:55Z

Jupreziosi:

[[Julia Preziosi]]

We don't have much time left.

Need to switch from clustering and discovering to exploring the ones we've found.
Build a compelling story.

We continued exploring the 44 genes via NCBI searches, inputting the data to our excel sheet and determining interesting status.

JP Mar 24 16

2016-03-24T17:44:11Z

Jupreziosi:

[[Julia Preziosi]]

We don't have much time left.

Need to switch from clustering and discovering to exploring the ones we've found.
Build a compelling story.

JP Mar 24 16

2016-03-24T17:42:33Z

Jupreziosi: Created page with "We don't have much time left. Need to switch from clustering and discovering to exploring the ones we've found. Build a compelling story."

We don't have much time left.

Need to switch from clustering and discovering to exploring the ones we've found.
Build a compelling story.

Julia Preziosi

2016-03-24T17:40:07Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:50:14Z

Jupreziosi:

[[Julia Preziosi]]

Using Generic GO Term Mapper with goa_human (Generic Go Slim) reference for 44 interesting genes:
only maps 22 of the genes by gene name.

http://go.princeton.edu/cgi-bin/GOTermMapper

QuickGO

http://www.ebi.ac.uk/QuickGO/GAnnotation

CateGOrizer

http://www.animalgenome.org/cgi-bin/util/gotreei

We are now analyzing the KEGG pathways of the 44 genes.

Input list of contig_gene names and sequences. Given a list of organisms; Blast BBH

http://www.genome.jp/kaas-bin/kaas_main?mode=user&mail=nielder@davidson.edu

'''Candidates:'''

Contig887_EIF4EBP1_Eukaryotic_translation_initiation_factor_4E-binding_protein_1_Bos_taurus

This gene encodes one member of a family of translation repressor proteins. The protein directly interacts with eukaryotic translation initiation factor 4E (eIF4E), which is a limiting component of the multisubunit complex that recruits 40S ribosomal subunits to the 5' end of mRNAs. Interaction of this protein with eIF4E inhibits complex assembly and represses translation. This protein is phosphorylated in response to various signals including UV irradiation and insulin signaling, resulting in its dissociation from eIF4E and activation of mRNA translation.

The protein leads to repression of transcription. It is upregulated in fed snakes.

it is involved in many signaling pathways.

ErbB receptors are typical cell membrane receptor tyrosine kinases that are activated following ligand binding and receptor dimerization... regulate cell proliferation, migration, differentiation, apoptosis, and cell motility.
Signaling through ErbB networks is modulated through dense positive and negative feedback and feed forward loops, including transcription-independent early loops and late loops mediated by newly synthesized proteins and miRNAs.

Clusters with:

JP Mar 22 16

2016-03-22T18:43:59Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:28:02Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:25:21Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:24:27Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:24:18Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:09:57Z

Jupreziosi:

JP Mar 22 16

2016-03-22T18:03:32Z

Jupreziosi:

JP Mar 22 16

2016-03-22T17:49:03Z

Jupreziosi:

JP Mar 22 16

2016-03-22T17:48:56Z

Jupreziosi:

JP Mar 22 16

2016-03-22T17:46:25Z

Jupreziosi: Created page with "Julia Preziosi Using Generic GO Term Mapper with goa_human (Generic Go Slim) reference for 44 interesting genes: only maps 22 of the genes by gene name."

[[Julia Preziosi]]

Using Generic GO Term Mapper with goa_human (Generic Go Slim) reference for 44 interesting genes:
only maps 22 of the genes by gene name.

Julia Preziosi

2016-03-22T17:34:41Z

Jupreziosi:

JP Mar 17 16

2016-03-17T18:54:45Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Wrote a code to extract gene id from a list of given gene names. Needed to manually search the gene id for the translated POUFs.

Resources:

Generic GO term Mapper:

http://go.princeton.edu/cgi-bin/GOTermMapper

using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo

*nothing

Using generic human given by website

*this looks promising

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

g:

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

JP Mar 17 16

2016-03-17T18:53:57Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resources:

Generic GO term Mapper:

http://go.princeton.edu/cgi-bin/GOTermMapper

using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo

*nothing

Using generic human given by website

*this looks promising

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

g:

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

JP Mar 17 16

2016-03-17T18:53:52Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resources:

Generic GO term Mapper:

http://go.princeton.edu/cgi-bin/GOTermMapper

using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo

*nothing

Using generic human given by website

*this looks promising

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

g:

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

JP Mar 17 16

2016-03-17T18:51:52Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resources:

Generic GO term Mapper:

http://go.princeton.edu/cgi-bin/GOTermMapper

using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo
*nothing
Using generic human given by website

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

g:

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

JP Mar 17 16

2016-03-17T18:32:41Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resources:

Generic GO term Mapper:

http://go.princeton.edu/cgi-bin/GOTermMapper

using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

g:

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

JP Mar 17 16

2016-03-17T18:05:04Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resources:

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

g:

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

JP Mar 17 16

2016-03-17T18:02:27Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resources:

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

CateGOrizer

http://www.animalgenome.org/bioinfo/tools/catego/

JP Mar 17 16

2016-03-17T17:59:37Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resource:

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

*this doesn't work on school computers

http://geneontology.org/page/go-slim-and-subset-guide

JP Mar 17 16

2016-03-17T17:48:50Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:

Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resource:

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. This script is an option of OWLTools, and it can be used to either create a new gene association file, which contains the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term."

http://geneontology.org/page/go-slim-and-subset-guide

JP Mar 17 16

2016-03-17T17:48:43Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:
Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resource:

Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. This script is an option of OWLTools, and it can be used to either create a new gene association file, which contains the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term."

http://geneontology.org/page/go-slim-and-subset-guide

JP Mar 17 16

2016-03-17T17:48:38Z

Jupreziosi:

[[Julia Preziosi]]

Wrote our first status report after our oral presentation on the 15th.

GO Slim:
Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.

Resource:
Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. This script is an option of OWLTools, and it can be used to either create a new gene association file, which contains the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term."

http://geneontology.org/page/go-slim-and-subset-guide

JP Mar 17 16

2016-03-17T17:42:59Z

Jupreziosi: Created page with "Julia Preziosi"

[[Julia Preziosi]]

Julia Preziosi

2016-03-17T17:40:41Z

Jupreziosi:

JP Mar 15 16

2016-03-17T17:40:29Z

Jupreziosi: Blanked the page

File:Clustering2.txt

2016-03-17T15:08:18Z

Jupreziosi:

File:Clustering1.txt

2016-03-17T15:08:07Z

Jupreziosi:

File:Renamer.txt

2016-03-17T15:07:50Z

Jupreziosi: Jupreziosi uploaded a new version of "File:Renamer.txt"

A python code that takes in raw fastq input and pulls out the sequence, adding an arbitrary label.

File:Refseqpouf.txt

2016-03-17T15:07:34Z

Jupreziosi:

File:POUFdict.txt

2016-03-17T15:07:21Z

Jupreziosi:

JP Resources

2016-03-17T15:07:01Z

Jupreziosi:

[[Julia Preziosi]]

Python Codes:

making a dictionary of POUF names
[[File:POUFdict.txt]]

(uses the file: [[File:refseqpouf.txt]] )

renaming the POUFs in the excel files (not needed)
[[File:renamer.txt]]

R Code:
1-1000 expression
0.01 Qval with heatmaps
[[File:clustering1.txt]]

1-1000 expression
0.001 Qval with heatmaps
[[File:clustering2.txt]]