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	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 844 to 893 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	green	network_comparison
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	328	Divided	1	258.437	235.183	1.09888
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	382	Subtracted		253.852	234.808	19.044
	428	Divided				1.0811
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	913	Subtracted		243.297	235.373	7.924
	990	Divided				1.03367
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	1290	Subtracted		228.644	223.736	4.908
	1365	Divided				1.02194
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	1089	Subtracted		218.487	212.656	5.831
	1126	Divided				1.02742
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]	1086	Subtracted		218.528	212.676	5.852
	1120	Divided				1.02752
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	1332	Subtracted		218.471	213.876	4.595
	1384	Divided				1.02148
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	990	Subtracted		221.682	228.68	6.998
	1035	Divided				1.03157
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698]	2913			0.00001	0.00001	1
		Subtracted		0	0	0
autoantigen ngp-1. [swissprot;acc:q13823]	573			250.302	236.817	13.485
	670	Divided				1.05694
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	1729			187.582	190.028	1.01304
	1816	Subtracted				2.446
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	1454			240.077	236.015	4.062
	1540	Divided				1.01721
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	2002	Subtracted		208.315	206.41	1.905
	2003	Divided				1.00923
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	1559			196.191	192.996	1.01655
	1632	Subtracted				3.195
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	2655	Divided		201.445	201.667	1.0011
	2661	Subtracted				0.222
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	1556	Divided		196.192	192.996	1.01656
	1630	Subtracted				3.196
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	980	Divided		130.289	134.713	1.03396
	1393	Subtracted				4.424
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	114			229.818	267.265	37.447
	181	Divided				1.16294
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	188	Subtracted		227.357	254.15	26.793
	244	Divided				1.11785
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	457	Subtracted		210.578	226.764	16.186
	464	Divided				1.07686
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	3117			0.00001	0.00001	1
		Subtracted		0	0	0
ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	2599	Divided		211.662	211.361	1.00142
	2625	Subtracted				0.301
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	307	Divided	0	1091	1021	1.06856
	483	Subtracted				70
	2125		1	217.871	219.366	1.495
	2148	Divided				1.00686
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]	2115			214.632	213.14	1.007
	2130	Subtracted				1.492
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	931	Divided		159.13	164.917	1.03637

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.