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

Results: HTML CSV LaTeX

Showing element 5158 to 5207 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2579	nitrilase 1. [refseq;acc:nm_005600]	Subtracted	213.422	213.75	0.328
2580	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]	Divided			1.00154
		Subtracted			0.328
2581	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	Divided	213.428	213.756	1.00154
		Subtracted			0.328
2582	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]	Divided	213.422	213.75	1.00154
		Subtracted			0.328
2583	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	Divided	213.415	213.743	1.00154
		Subtracted			0.328
2584	dystrophin. [swissprot;acc:p11532]	Divided	213.422	213.75	1.00154
		Subtracted			0.328
2585	angiomotin. [refseq;acc:nm_133265]	Divided			1.00154
		Subtracted			0.328
2586	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]	Divided			1.00154
		Subtracted			0.328
2587	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]	Divided			1.00154
		Subtracted			0.328
2588	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	Divided	222.305	222.64	1.00151
	polybromo 1. [refseq;acc:nm_018165]	Subtracted	220.02	219.696	0.324
2589	membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792]	Divided	212.74	212.422	1.0015
	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	Subtracted	220.02	219.696	0.324
2590	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]
	proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062]	Divided	214.605	214.287	1.00148
2591	polybromo 1. [refseq;acc:nm_018165]		220.02	219.696	1.00147
	possible global transcription activator snf2l1. [swissprot;acc:p28370]	Subtracted			0.324
2592	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	Divided			1.00147
	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]	Subtracted			0.324
2593	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]
	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	Divided			1.00147
2594	membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792]	Subtracted	212.74	212.422	0.318
	possible global transcription activator snf2l1. [swissprot;acc:p28370]	Divided	220.02	219.696	1.00147
2595	proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062]	Subtracted	214.605	214.287	0.318
	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]	Divided	220.02	219.696	1.00147
2596	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	Subtracted	224.875	225.192	0.317
	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]	Divided	220.02	219.696	1.00147
2597	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	Subtracted	224.877	225.193	0.316
	ran binding protein 11. [refseq;acc:nm_016338]	Divided	212.711	212.401	1.00146
2598		Subtracted			0.31
	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	Divided	202.142	202.436	1.00145
2599	ba207c16.2 (fragment). [sptrembl;acc:q9nql7]		211.662	211.361	1.00142
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Subtracted	224.891	225.195	0.304
2600	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	Divided	224.877	225.193	1.00141
	zinc finger protein 258. [refseq;acc:nm_145310]	Subtracted	224.891	225.195	0.304
2601	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	Divided	214.502	214.2	1.00141
	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	Subtracted	224.891	225.195	0.304
2602	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	Divided	224.875	225.192	1.00141
	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	Subtracted	224.891	225.195	0.304
2603	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	Divided	214.494	214.192	1.00141
2604	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	Subtracted	224.891	225.195	0.304

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.