MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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description	Rank	Gene	Value Type	green	Interaction Map	Filtered	Network Comparison Type	network_comparison	red

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Showing element 3682 to 3731 of 66312 in total

Filtered  : 1

description	Rank	Value Type	green	Interaction Map	Network Comparison Type	network_comparison	red
adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3]	2060	Measured	5865.84	High confidence	Divided	1.0564	5552.69
	2077	Squared	27764.1			1.08957	25481.8
	2088	Measured	5865.84		Subtracted	313.15	5552.69
	2440	Rooted	61.2677		Divided	1.01415	60.4127
					Subtracted	0.855
	2492	Squared	43030.6	Low confidence		1645.7	44676.3
	2544				Divided	1.03824
adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]	268	Rooted	74.0605		Subtracted	3.8985	70.162
	275				Divided	1.05556
	351	Measured	8038.01			1.05489	7619.78
	352	Ranked	197.135			1.03869	204.762
					Subtracted	7.627
	419	Measured	8038.01			418.23	7619.78
	4389	Squared	41239		Divided	1.02313	42192.8
	4442				Subtracted	953.8
adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973]	265	Rooted	74.0605			3.8985	70.162
	272				Divided	1.05556
	348	Measured	8038.01			1.05489	7619.78
	349	Ranked	197.135			1.03869	204.762
					Subtracted	7.627
	416	Measured	8038.01			418.23	7619.78
	4385	Squared	41239		Divided	1.02313	42192.8
	4439				Subtracted	953.8
adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851]	421	Ranked	200.076			6.988	207.064
	437				Divided	1.03493
	472	Rooted	73.2628			1.04558	70.0689
	534				Subtracted	3.1939
	1023	Measured	8009.78		Divided	1.03796	7716.88
	1142				Subtracted	292.9
	1575	Ranked	225.675	High confidence		3.572	222.103
	1600				Divided	1.01608
	1789	Squared	27794.9		Subtracted	2284.7	25510.2
	2050	Measured	5870.11		Divided	1.05647	5556.36
	2082	Squared	27794.9			1.08956	25510.2
	2083	Measured	5870.11		Subtracted	313.75	5556.36
	2429	Rooted	61.2917		Divided	1.01426	60.43
	2430				Subtracted	0.8617
	2836	Squared	42345.3	Low confidence	Divided	1.03661	43895.6
	2944				Subtracted	1550.3
adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]	1506		40846.2		Divided	1.04347	42621.6
	1956				Subtracted	1775.4
	2044	Ranked	198.24	High confidence	Divided	1.00851	199.928
	2071				Subtracted	1.688
	2349	Rooted	70.0808			1.1367	68.9441
	2376				Divided	1.01649
	2563	Measured	6916.14		Subtracted	100.9	6815.24
	2623				Divided	1.01481
	2689	Squared	29898.1		Subtracted	335.1	30233.2
	2726				Divided	1.01121
	4176	Measured	7651.78	Low confidence		1.02049	7498.13

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.