Notes 2/16/16 - Revision history

Ktsmith at 18:45, 23 February 2016

2016-02-23T18:45:00Z

Ktsmith at 18:44, 23 February 2016

2016-02-23T18:44:46Z

Ktsmith at 19:56, 18 February 2016

2016-02-18T19:56:59Z

Ktsmith at 19:17, 18 February 2016

2016-02-18T19:17:53Z

Ktsmith at 19:12, 18 February 2016

2016-02-18T19:12:39Z

Ktsmith at 19:09, 18 February 2016

2016-02-18T19:09:06Z

Ktsmith at 19:08, 18 February 2016

2016-02-18T19:08:25Z

Ktsmith at 19:06, 18 February 2016

2016-02-18T19:06:07Z

Ktsmith at 19:05, 18 February 2016

2016-02-18T19:05:14Z

Ktsmith at 19:55, 16 February 2016

2016-02-16T19:55:59Z

@@ Line 30: / Line 30: @@
 * GATA6 (Regulates proximal-distal identity in the intestines) 1) 32.2 2) 33.96 3) 19.17 4) 37.87 5) 31.67 6) 31.98
 * MYBL2 (Regulates commitment of colon stem cells to differentiate) 1) 0.04 2) 0 3) 0.05 4) 0 5) 0 6) 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 5) 3.07
+* 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 6) 3.07
 * 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)

@@ Line 9: / Line 9: @@
 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 4: SLC6A19 (FPKM 13213.57), SLC15A1 (FPKM 14316.17), maltase/sucrase (FPKM 747.19) aminopeptidase (FPKM 556.07)
-Snake 5: SLC15A1, SLC6A19, sucrase/maltase (1054.27) , aminopeptidase (513.37)
+Snake 5: SLC15A1 (FPKM 11347.62), SLC6A19 (FPKM 4130.4), sucrase/maltase (FPKM 1054.27) , aminopeptidase (FPKM 513.37)
-Snake 6: SLC15A1, SLC6A19, sucrase/maltase, aminopeptidase
+Snake 6: SLC15A1 (FPKM 9310.97), SLC6A19 (FPKM 6632.26), sucrase/maltase (FPKM 735.21), aminopeptidase (FPKM 488.85)
 '''Housekeeping genes'''
@@ Line 28: / Line 28: @@
 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
+* GATA6 (Regulates proximal-distal identity in the intestines) 1) 32.2 2) 33.96 3) 19.17 4) 37.87 5) 31.67 6) 31.98
-* MYBL2 (Regulates commitment of colon stem cells to differentiate) 1) 0.04 2) 0 3) 0.05 4) 0 5) 0
+* MYBL2 (Regulates commitment of colon stem cells to differentiate) 1) 0.04 2) 0 3) 0.05 4) 0 5) 0 6) 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
+* 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 5) 3.07
 * 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)

@@ Line 3: / Line 3: @@
 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, (SLC1A5 very very low expression, might just mean that duodenum or ileum)
+Snake 3: SLC15A1 (FPKM 14322.98), SLC6A19 (FPKM 5695.09), sucrase/maltase (FPKM 1430.56), Aminopeptidase (FPKM 426.59)
-Snake 4: SLC6A19, SLC15A1, (SLC1A5 very low expression)
+Snake 4: SLC6A19 (13213.57), SLC15A1 (14316.17), maltase/sucrase (747.19) aminopeptidase (556.07)
-Snake 5: SLC15A1, fairly high expression of SLC6A19, (SLC1A5 very low expression)
+Snake 5: SLC15A1, SLC6A19, sucrase/maltase (1054.27) , aminopeptidase (513.37)
-Snake 6: SLC15A1, SLC6A19, (SLC1A5 very low expression)
+Snake 6: SLC15A1, SLC6A19, sucrase/maltase, aminopeptidase
 '''Housekeeping genes'''
@@ Line 21: / Line 21: @@
 SLC15A1 protein coding gene: encodes an ''intestinal'' hydrogen peptide cotransporter that is a member of the solute carrier family 15
-ASCT2 (SLC1A5) expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum
+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

← Older revision		Revision as of 19:17, 18 February 2016
Line 23:		Line 23:
	ASCT2 (SLC1A5) expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum		ASCT2 (SLC1A5) expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum

−	STX2	+	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
−
−	COL3A1
−
−	GPBAR1

← Older revision		Revision as of 19:12, 18 February 2016
Line 22:		Line 22:

	ASCT2 (SLC1A5) expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum		ASCT2 (SLC1A5) expressed in the kidney but expression is high in the jejunum and colon but lower in duodenum and ileum
		+
		+	STX2
		+
		+	COL3A1
		+
		+	GPBAR1