Difference between revisions of "Notes 2/16/16"
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over-expressed sequences match: | over-expressed sequences match: | ||
| − | Snake 1: matches with an mRNA sequence from an intestine sample of an elephant fish, SLC15A1, SLC6A19 | + | Snake 1: matches with an mRNA sequence from an intestine sample of an elephant fish, SLC15A1 (FPKM 14366.5) , SLC6A19 (FPKM 7306.48), Aminopeptidase (FPKM 494.97) sucrase/maltase (FPKM 935.83) |
| − | Snake 2: SLC15A1, SLC6A19 | + | Snake 2: SLC15A1 (FPKM 13466.62), SLC6A19 (FPKM 4132.78), sucrase/maltase (FPKM 1133.27), Aminopeptidase (FPKM 432.93) |
| − | Snake 3: SLC15A1, SLC6A19, ( | + | Snake 3: SLC15A1 (FPKM 14322.98), SLC6A19 (FPKM 5695.09), sucrase/maltase (FPKM 1430.56), Aminopeptidase (FPKM 426.59) |
| − | Snake 4: SLC6A19, SLC15A1, ( | + | Snake 4: SLC6A19 (13213.57), SLC15A1 (14316.17), maltase/sucrase (747.19) aminopeptidase (556.07) |
| − | Snake 5: SLC15A1, | + | Snake 5: SLC15A1, SLC6A19, sucrase/maltase (1054.27) , aminopeptidase (513.37) |
| − | Snake 6: SLC15A1, SLC6A19, | + | Snake 6: SLC15A1, SLC6A19, sucrase/maltase, aminopeptidase |
'''Housekeeping genes''' | '''Housekeeping genes''' | ||
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SLC15A1 protein coding gene: encodes an ''intestinal'' hydrogen peptide cotransporter that is a member of the solute carrier family 15 | SLC15A1 protein coding gene: encodes an ''intestinal'' hydrogen peptide cotransporter that is a member of the solute carrier family 15 | ||
| − | + | Amino peptidase (Aspartyl_aminopeptidase_Homo_sapiens): source small intestine, products are amino acids and peptides | |
| − | STX2, COL3A1, GPBAR1: all from Castoe et al paper; examples of genes that have experienced positive selection (P < 0.001) on snake lineages and are related to prominent phenotypic or cellular traits of snakes- HOWEVER NOT HIGHLY EXPRESSED IN ANY OF OUR SNAKES | + | maltase/sucrose (Si_Sucrase-isomaltase,_intestinal_Rattus_norvegicus) : source small intestine, products are glucose and fructose |
| + | |||
| + | '''Housekeeping genes that weren't highly expressed''' | ||
| + | |||
| + | Important to note than many housekeeping genes for intestines were not extremely highly expressed at all in our samples, not as great evidence as was found for the liver samples | ||
| + | * GATA6 (Regulates proximal-distal identity in the intestines) 1) 32.2 2) 33.96 3) 19.17 4) 37.87 5) 31.67 | ||
| + | * MYBL2 (Regulates commitment of colon stem cells to differentiate) 1) 0.04 2) 0 3) 0.05 4) 0 5) 0 | ||
| + | * ASCT2 (SLC1A5 expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum) 1) 2.29 2) 2.96 3) 2.65 4) 1.39 5) 3.75 | ||
| + | * STX2, COL3A1, GPBAR1: all from Castoe et al paper; examples of genes that have experienced positive selection (P < 0.001) on snake lineages and are related to prominent phenotypic or cellular traits of snakes- HOWEVER NOT HIGHLY EXPRESSED IN ANY OF OUR SNAKES (range of FPKM from 0 - 4) | ||
Revision as of 19:56, 18 February 2016
Looking for housekeeping intestine genes so that we can make sure our samples are accurate
over-expressed sequences match:
Snake 1: matches with an mRNA sequence from an intestine sample of an elephant fish, SLC15A1 (FPKM 14366.5) , SLC6A19 (FPKM 7306.48), Aminopeptidase (FPKM 494.97) sucrase/maltase (FPKM 935.83)
Snake 2: SLC15A1 (FPKM 13466.62), SLC6A19 (FPKM 4132.78), sucrase/maltase (FPKM 1133.27), Aminopeptidase (FPKM 432.93)
Snake 3: SLC15A1 (FPKM 14322.98), SLC6A19 (FPKM 5695.09), sucrase/maltase (FPKM 1430.56), Aminopeptidase (FPKM 426.59)
Snake 4: SLC6A19 (13213.57), SLC15A1 (14316.17), maltase/sucrase (747.19) aminopeptidase (556.07)
Snake 5: SLC15A1, SLC6A19, sucrase/maltase (1054.27) , aminopeptidase (513.37)
Snake 6: SLC15A1, SLC6A19, sucrase/maltase, aminopeptidase
Housekeeping genes
BOAT1 (SLC6A19) solute carrier family 6 (neutral amino acid transporter), member 19, mRNA (housekeeping gene BOAT1) found in intestine and kidney
SLC15A1 protein coding gene: encodes an intestinal hydrogen peptide cotransporter that is a member of the solute carrier family 15
Amino peptidase (Aspartyl_aminopeptidase_Homo_sapiens): source small intestine, products are amino acids and peptides
maltase/sucrose (Si_Sucrase-isomaltase,_intestinal_Rattus_norvegicus) : source small intestine, products are glucose and fructose
Housekeeping genes that weren't highly expressed
Important to note than many housekeeping genes for intestines were not extremely highly expressed at all in our samples, not as great evidence as was found for the liver samples
- GATA6 (Regulates proximal-distal identity in the intestines) 1) 32.2 2) 33.96 3) 19.17 4) 37.87 5) 31.67
- MYBL2 (Regulates commitment of colon stem cells to differentiate) 1) 0.04 2) 0 3) 0.05 4) 0 5) 0
- ASCT2 (SLC1A5 expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum) 1) 2.29 2) 2.96 3) 2.65 4) 1.39 5) 3.75
- STX2, COL3A1, GPBAR1: all from Castoe et al paper; examples of genes that have experienced positive selection (P < 0.001) on snake lineages and are related to prominent phenotypic or cellular traits of snakes- HOWEVER NOT HIGHLY EXPRESSED IN ANY OF OUR SNAKES (range of FPKM from 0 - 4)
