{
"metadata": {
"name": "CC_ampk"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": "Searching for info on AMP-activated protein kinase in oysters / qDOD"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "![pw](http://www.cellsignal.com/reference/pathway/images/AMPK.jpg)"
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": "SQLShare"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "```\nSELECT * \n FROM [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]\n where Description like '%AMP-activated%'\n```"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "CGI_ID|SPID|evalue|Description \nCGI_10003983|Q28948|0|5'-AMP-activated protein kinase catalytic subunit alpha-2 \nCGI_10010273|Q91WG5|4E-36|5'-AMP-activated protein kinase subunit gamma-2 \nCGI_10010275|Q91WG5|1E-128|5'-AMP-activated protein kinase subunit gamma-2 \nCGI_10016569|Q9QZH4|2E-09|5'-AMP-activated protein kinase subunit beta-2 \nCGI_10021816|Q5RDH5|5E-15|5'-AMP-activated protein kinase catalytic subunit alpha-1 \nCGI_10025389|Q6PAM0|3E-84|5'-AMP-activated protein kinase subunit beta-2 \n "
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": "Emma's Proteomic Data"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "```\nSELECT * FROM [sr320@washington.edu].[OABS_ETS_S3]\nWhere [Gene Name] like '%AMP-activated protein kinase%'\n```"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Q6PAM0 \n3e-84 \n5'-AMP-activated protein kinase subunit beta-2 "
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": "OsHV\n"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "```\nSELECT * FROM [sr320@washington.edu].[Cgigas Larvae RNA-Seq OsHV]\n where ID like 'CGI_10003983'\n``` "
},
{
"cell_type": "raw",
"metadata": {},
"source": "CGI_10003983\n165\n165\n18.094\nCGI_10003983\nQ28948\n0\n5'-AMP-activated protein kinase catalytic subunit alpha-2"
},
{
"cell_type": "heading",
"level": 3,
"metadata": {},
"source": "more on CGI_10003983"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "```\nSELECT * FROM [sr320@washington.edu].[qDOD_v9_gene]\n where Column9 like '%CGI_10003983%'\n```"
},
{
"cell_type": "raw",
"metadata": {},
"source": "scaffold1375\nGLEAN\nmRNA\n40162\n57556\n1\n+\n.\nID=CGI_10003983;\n"
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": "IGV Genome Browser"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Loading session `http://eagle.fish.washington.edu/cnidarian/oyster_v9_igv_session.xml`"
},
{
"cell_type": "markdown",
"metadata": {},
"source": ""
},
{
"cell_type": "markdown",
"metadata": {},
"source": ""
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": "Oyster Genome Browser"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "\n"
},
{
"cell_type": "code",
"collapsed": false,
"input": "",
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}