GcatWiki - User contributions [en]

NHE Apr 5 Notes

2016-04-05T18:57:02Z

Nielder: Created page with "Nick Elder Group 2 intestines We just went to watch the pythons feed. Wow. I jumped. Every. Single. Time. ankyrin repeats in NOTCH and PPP1R16A Mfap2 (MAG1) invol..."

[[Nick Elder]]

[[Group 2 intestines]]

We just went to watch the pythons feed. Wow. I jumped. Every. Single. Time.

ankyrin repeats in NOTCH and PPP1R16A

Mfap2 (MAG1) involved in NOTCH and TGF - beta signaling pathways.

Functional roles of TGF-β1 in intestinal epithelial cells through Smad-dependent and non-Smad pathways.

Microfibrillar Proteins MAGP-1 and MAGP-2 Induce Notch1 Extracellular Domain Dissociation and Receptor Activation

Nick Elder

2016-04-05T18:10:35Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

[[NHE Feb 4 Notes]]

[[NHE Feb 9 Notes]]

[[NHE Feb 23 Notes]]

[[NHE Feb 25 Notes]]

[[NHE Mar 8 Notes]]

[[NHE Mar 10 Notes]]

[[NHE Mar 17 Notes]]

[[NHE Mar 22 Notes]]

[[NHE Mar 24 Notes]]

[[NHE Mar 31 Notes]]

[[NHE Apr 5 Notes]]

File of 44 interesting genes and GO IDs [[File:Genes_of_interest_44.txt]]

Nick Elder

2016-03-31T17:41:30Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

[[NHE Feb 4 Notes]]

[[NHE Feb 9 Notes]]

[[NHE Feb 23 Notes]]

[[NHE Feb 25 Notes]]

[[NHE Mar 8 Notes]]

[[NHE Mar 10 Notes]]

[[NHE Mar 17 Notes]]

[[NHE Mar 22 Notes]]

[[NHE Mar 24 Notes]]

[[NHE Mar 31 Notes]]

File of 44 interesting genes and GO IDs [[File:Genes_of_interest_44.txt]]

NHE Mar 24 Notes

2016-03-24T18:53:54Z

Nielder: Created page with "Nick Elder Group 2 intestines Doing supervised clustering with a down regulated gene. (ITPA - from the 6 highly differentiated genes) Setting the threshold value to..."

[[Nick Elder]]

[[Group 2 intestines]]

Doing supervised clustering with a down regulated gene. (ITPA - from the 6 highly differentiated genes)

Setting the threshold value to 0.0256 produces correct clustering vs 0.0257 which has improper clustering.
The gene that makes the difference is INTS7

Also did supervised clustering around LGR5 (Campbell recommended)

Re-did clustering generally with mean range from 1 to 10000 and qvals = 0.01

Found a list of 44 genes, but not all the same. 6 do not overlap. Don't know why. Have that list.

Doing KAAS for ITPA (down regulated) and 44 genes found with the larger range

want to do more specific data mining with the GO IDs and KEGG Pathways

Nick Elder

2016-03-24T16:08:58Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

[[NHE Feb 4 Notes]]

[[NHE Feb 9 Notes]]

[[NHE Feb 23 Notes]]

[[NHE Feb 25 Notes]]

[[NHE Mar 8 Notes]]

[[NHE Mar 10 Notes]]

[[NHE Mar 17 Notes]]

[[NHE Mar 22 Notes]]

[[NHE Mar 24 Notes]]

File of 44 interesting genes and GO IDs [[File:Genes_of_interest_44.txt]]

Nick Elder

2016-03-24T16:08:46Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

[[NHE Feb 4 Notes]]

[[NHE Feb 9 Notes]]

[[NHE Feb 23 Notes]]

[[NHE Feb 25 Notes]]

[[NHE Mar 8 Notes]]

[[NHE Mar 10 Notes]]

[[NHE Mar 17 Notes]]

[[NHE Mar 22 Notes]]

NHE Mar 24 Notes]]

File of 44 interesting genes and GO IDs [[File:Genes_of_interest_44.txt]]

NHE Mar 22 Notes

2016-03-22T17:49:05Z

Nielder: Created page with "Nick Elder Group 2 intestines DESeq only cares about raw number of reads (expected count) and not RPKM or FPKM standardization because it compares within the gene, n..."

[[Nick Elder]]

[[Group 2 intestines]]

DESeq only cares about raw number of reads (expected count) and not RPKM or FPKM standardization because it compares within the gene, not between genes.

Nick Elder

2016-03-22T17:33:13Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

[[NHE Feb 4 Notes]]

[[NHE Feb 9 Notes]]

[[NHE Feb 23 Notes]]

[[NHE Feb 25 Notes]]

[[NHE Mar 8 Notes]]

[[NHE Mar 10 Notes]]

[[NHE Mar 17 Notes]]

[[NHE Mar 22 Notes]]

File of 44 interesting genes and GO IDs [[File:Genes_of_interest_44.txt]]

NHE Mar 17 Notes

2016-03-17T18:28:38Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

Last Tuesday we had presentations.

Uploaded python script and sample files under JP Resources (Julia Preziosi's page)

File:Genes of interest 44.txt

2016-03-17T18:21:54Z

Nielder:

Nick Elder

2016-03-17T18:21:44Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

[[NHE Feb 4 Notes]]

[[NHE Feb 9 Notes]]

[[NHE Feb 23 Notes]]

[[NHE Feb 25 Notes]]

[[NHE Mar 8 Notes]]

[[NHE Mar 10 Notes]]

[[NHE Mar 17 Notes]]

File of 44 interesting genes and GO IDs [[File:Genes_of_interest_44.txt]]

Nick Elder

2016-03-17T18:21:16Z

Nielder:

NHE Mar 17 Notes

2016-03-17T18:18:28Z

Nielder: Created page with "Nick Elder Group 2 intestines Last Tuesday we had presentations."

[[Nick Elder]]

[[Group 2 intestines]]

Last Tuesday we had presentations.

File:Sample3.txt

2016-03-17T18:17:20Z

Nielder:

File:Sample2.txt

2016-03-17T18:17:05Z

Nielder:

File:Sample1.txt

2016-03-17T18:16:53Z

Nielder:

File:GO term no repeat and list PTHONSCRIPT.txt

2016-03-17T18:16:19Z

Nielder:

JP Resources

2016-03-17T18:15:54Z

Nielder:

[[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]]

Stripping repeat GO IDs from contigs and generating list of all IDs
[[File:GO_term_no_repeat_and_list_PTHONSCRIPT.txt]]

Sample input file [[File:sample1.txt]]

Sample output file 1 [[File:sample2.txt]]

Sample output file 2 [[File:sample3.txt]]

JP Resources

2016-03-17T18:15:33Z

Nielder:

[[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]]

Stripping repeat GO IDs from contigs and generating list of all IDs
[[File:GO_term_no_repeat_and_list_PTHONSCRIPT.txt]]
Sample input file [[File:sample1.txt]]
Sample output file 1 [[File:sample2.txt]]
Sample output file 2 [[File:sample3.txt]]

Nick Elder

2016-03-17T17:40:05Z

Nielder:

NHE Mar 10 Notes

2016-03-10T19:19:42Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

Used supervised clustering again, setting the range between 1 and 1000 and setting the myQvals to 0.001.

Found only 6 genes (including 2 POUFs from yesterday

*DNA polymerase subunit
*secretory protein
*2 inosine related genes (necessary for guanine synthesis)
*mitochondrial gene for NAD (necessary for metabolism)
*translation initiation factor (attract 40s subunit of ribosomes)

only thing is, the graph clusters wrong

NHE Mar 10 Notes

2016-03-10T19:19:17Z

Nielder:

NHE Mar 8 Notes

2016-03-10T19:09:24Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

POUFS cannot be changed in the files because it breaks code. The gene names have to match exactly how they appears in the reference genome. Made reference excel file instead and uploaded to wiki

Our new direction:

*look at absolute changes in expression levels (genes that go from on to off and off to on)

ran the normalized plot with raw scores with Q-vals set to 0.01.

38 potential genes

Potential genes:
*JAGN1 - was one of the POUFs. no expression in non fed. slight increase in fed. secretory protein. necessary for neutrophil survival...
**POUF 2542
*CYP2J2 - down regulated in Fed
*NDUFB6 - mitochondrial. upregulated in fed. responsible for NADH oxidation.
**POUF 544

Is NAD production significantly upregulated?

NHE Mar 10 Notes

2016-03-10T18:45:18Z

Nielder: Created page with "Nick Elder Group 2 intestines"

[[Nick Elder]]

[[Group 2 intestines]]

Nick Elder

2016-03-10T18:40:22Z

Nielder:

NHE Mar 8 Notes

2016-03-08T19:56:36Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

POUFS cannot be changed in the files because it breaks code. The gene names have to match exactly how they appears in the reference genome. Made reference excel file instead and uploaded to wiki

Our new direction:

*look at absolute changes in expression levels (genes that go from on to off and off to on)

ran the normalized plot with raw scores with Q-vals set to 0.01.

38 potential genes

Potential genes:
*JAGN1 - was one of the POUFs. no expression in non fed. slight increase in fed. secretory protein. necessary for neutrophil survival...
*CYP2J2 - down regulated in Fed
*NDUFB6 - POUF. mitochondrial. upregulated in fed. responsible for NADH oxidation.

Is NAD production significantly upregulated?

NHE Mar 8 Notes

2016-03-08T19:31:36Z

Nielder:

NHE Mar 8 Notes

2016-03-08T18:38:12Z

Nielder: Created page with "Nick Elder Group 2 intestines"

[[Nick Elder]]

[[Group 2 intestines]]

Nick Elder

2016-03-08T18:35:50Z

Nielder:

NHE Feb 25 Notes

2016-02-25T19:56:31Z

Nielder: Created page with "Nick Elder Group 2 intestines We will work on changing the proteins of unknown function to actual protein names in the 12 lists WE REPLACED THE NAMES OF THE POUFS ..."

[[Nick Elder]]

[[Group 2 intestines]]

We will work on changing the proteins of unknown function to actual protein names in the 12 lists

WE REPLACED THE NAMES OF THE POUFS WITH PROTEIN NAMES IN ALL 12 EXCEL FILES

Nick Elder

2016-02-25T18:38:58Z

Nielder:

NHE Feb 23 Notes

2016-02-23T19:58:31Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

used Blast2GO Pro to Blast the proteins of unknown function agains 2 protein reference databases

got some good lists

time is up. gotta go.

NHE Feb 23 Notes

2016-02-23T19:57:18Z

Nielder: Created page with "Nick Elder Group 2 intestines"

[[Nick Elder]]

[[Group 2 intestines]]

Nick Elder

2016-02-23T18:38:31Z

Nielder:

Nick Elder

2016-02-18T18:48:06Z

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Nick Elder

2016-02-11T18:40:14Z

Nielder:

NHE Feb 9 Notes

2016-02-09T19:35:36Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

Clustering:
*Grouping genes, samples, etc.
**may present the order in a way that does not reflect how would would expect/want it to
*Can be used to pull out patterns and make predictions
*Induction can look much more dramatic than repression
*Changing the y-axis to a logarithmic scale reveals much more drastic changes in repression
**Similar relationships could be caused by direct interaction or co-regulation
**Strong negative correlation could be as interesting as positive correlation
***Computers are more likely to group positive correlations
*Gene Expression Profiles (Guilt by Association)
**comparing genes or expression levels in samples over time
**Correlation, Euclidean distance, Hamming Distance, etc....
**Correlation is very sensitive to outliers; also, very small changes, possibly due to noise, can be interpreted as correlation with more drastic changes
*Linkage Methods
**Can take the nucleus/average of a cluster and compare that to a desired single gene
**Can average all the distances between all points
**Can compare the gene of interest to all the rest of the genes individually

*Hierarchical clustering
**Joins two most similar genes
**Join next two most similar "objects" (genes or clusters of genes)
**Repeat until all genes have been joined
**Once clustered, two genes can, under no circumstances, under penalty of death, in no way possible on heaven or earth, be split apart
**No gene left behind. Everyone has to be in the cluster; starts at +1 correlation and end at -1 correlation
***Genes that are most distant in the cluster (opposite correlation) could be co-regulated together
**Cutting the tree
***Draw a line to separate the clusters
****Decision to cut the line is completely arbitrary
*K-means Clustering
**Specify how many clusters to form - just break into groups, not breaking the tree
**Randomly assign each gene to one of K different clusters
**Average expression of all genes in each cluster to create K pseudo genes
**Rearrange genes by assigning each other to the cluster represented by the pseudo gene to which it is most similar
**Repeat until convergence
*Supervised Clustering
**Find genes in expression file whose patterns are highly similar to a desired gene or pattern
**Add closest gene first
**Then add gene that is closest to all genes already in cluster
**Repeat, as long as added gene is within specified distance to genes already in the cluster
**Distance from one gene to a set of genes defined to be maximum (or minimum or average) of all distances to individual members of the set (complete, single, and average linkage, respectively)
**Dr. C says that it might be really nice to cluster genes that move with a transcription factor, since a little induction in the transcription factor can have major effects on other gene expression
*Quality Clustering: QT Clust
**Each gene builds a supervised cluster
**Gene with "best" list, and genes in its list, becomes the next cluster
**Remove these genes from consideration, and repeat
**Stop when all genes are clustered, or largest cluster is smaller than user specified threshold
**Make 'cliques', find the largest, separate that group, remove all members from that group from all other groups, and make the next largest group from the existing members.

NHE Feb 9 Notes

2016-02-09T18:39:26Z

Nielder: Created page with "Nick Elder Group 2 intestines"

[[Nick Elder]]

[[Group 2 intestines]]

Nick Elder

2016-02-09T18:39:07Z

Nielder:

NHE Feb 4 Notes

2016-02-04T19:56:49Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

Questions to think about:

1. What are we trying to get and how will we get there?
*What is the gene that triggers/begins the cascade of physiological changes in the small intestine?
*Would be ideal if we could find a specific process that the differentially regulated genes control
*Is the responsible gene only turned on or off for a small time range (quick switch) or does it stay on or off for a long period of time?

2. What do we need to do with each of the 12 data sets to be able to evaluate them later?
*Look for housekeeping genes or tissue specific genes
*If possible, confirm that we have the mucosa vs serosa
*instead of looking at differential expression first, could search by function as determined by GO

http://www.proteinatlas.org/search/tissue_specificity_rna:small%20intestine;tissue+enriched+AND+show_columns:groupenriched

NHE Feb 4 Notes

2016-02-04T19:34:41Z

Nielder:

NHE Feb 4 Notes

2016-02-04T19:09:53Z

Nielder: Created page with "Nick Elder Group 2 intestines Questions to think about: 1. What are we trying to get and how will we get there? *What is the gene that triggers/begins the cascade ..."

NHE Feb 2 Notes

2016-02-04T18:46:26Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

BLAST Results:
*most were mitochondrial

We can download the sequences from the 2015 paper, but not the list of genes
2013 Paper has list of genes with gene ontology

We are using DESeq standard to normalize(?) data
*used to normalize expression
**normalizes for the length of the gene per million reads
**FPKM values

Used R and DESeq data to generate heat maps of differentially expressed genes in both liver and intestine.

Also tired to separate fed and fasted within the liver and intestine groups. (Modified R code)

*noticed that one of the fed (animal 4?) was being grouped as more similar to the fasted animals than the other fed.

NHE Feb 2 Notes

2016-02-04T18:46:15Z

Nielder:

[[Nick Elder]]

[[Group 2 intestines]]

BLAST Results:
*most were mitochondrial

We can download the sequences from the 2015 paper, but not the list of genes
2013 Paper has list of genes with gene ontology

We are using DESeq standard to normalize(?) data
*used to normalize expression
**normalizes for the length of the gene per million reads
**FPKM values

Used R and DESeq data to generate heat maps of differentially expressed genes in both liver and intestine
Also tired to separate fed and fasted within the liver and intestine groups. (Modified R code)

*noticed that one of the fed (animal 4?) was being grouped as more similar to the fasted animals than the other fed.

Nick Elder

2016-02-04T18:41:53Z

Nielder:

NHE Feb 2 Notes

2016-02-04T18:41:32Z

Nielder:

NHE Feb 2 Notes

2016-02-04T18:41:20Z

Nielder:

Nick Elder

2016-02-04T18:37:45Z

Nielder:

cool science stuff. yeah.

Notes

[[Group 2 intestines]]

[[NHE Jan 12 Notes]]

[[NHE Jan 14 Notes]]

[[NHE Jan 19 Notes]]

[[NHE Jan 21 Notes]]

[[NHE Jan 26 Notes]]

[[NHE Feb 2 Notes]]

Nick Elder

2016-02-04T18:37:06Z

Nielder:

NHE Feb 2 Notes

2016-02-02T19:55:35Z

Nielder: Created page with "Nick Elder Group 2 intestines BLAST Results: *most were mitochondrial We can download the sequences from the 2015 paper, but not the list of genes 2013 Paper has l..."