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

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Showing element 5408 to 5457 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
338	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	Squared	Divided	1	46785.7	58383.2	1.24789
339	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	Rooted	Subtracted	0	28.0711	26.8141	1.257
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]			1	52.7936	60.0592	7.2656
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked	Divided		243.583	267.527	1.0983
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Measured	Subtracted	0	1049.21	989.438	59.772
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Ranked		1	200.691	179.88	20.811
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Squared		0	188.176	230.603	42.427
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Measured	Divided		996.883	1070.03	1.07338
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Rooted			29.6274	31.1837	1.05253
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured		1	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Squared			46785.7	58383.2	1.24789
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]			0	3680.04	3222.31	1.14205
	neuralized-like. [refseq;acc:nm_004210]	Measured	Subtracted	1	1657.68	2690.25	1032.57
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Rooted	Divided		77.5797	70.0179	1.108
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Ranked	Subtracted	0	7163.55	7759.61	596.06
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]		Divided		10344.1	10903.3	1.05406
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Squared	Subtracted	1	28895.6	35572.8	6677.2
340	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	Ranked			239.75	260.544	20.794
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]			0	8123.75	8719	595.25
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Measured			1048.65	988.882	59.768
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]		Divided		559.333	600	1.07271
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Ranked			11372.3	10792.3	1.05374
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Rooted			29.6283	31.1839	1.0525
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured		1	20446.1	24136.4	1.18049
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Squared		0	3680.04	3222.31	1.14205
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Ranked		1	235.383	258.476	1.09811
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Rooted			58.4926	64.8047	1.10791
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Squared			32117	40054	1.24713
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Measured	Subtracted		11743.3	10712.3	1031
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Squared		0	1967.66	1925.55	42.11
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Rooted		1	45.7414	52.932	7.1906
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]			0	12.9585	14.1963	1.2378
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared		1	28895.6	35572.8	6677.2
341	60s ribosomal protein l12. [swissprot;acc:p30050]	Rooted		0	27.5183	28.7547	1.2364
	60s ribosomal protein l9. [swissprot;acc:p32969]	Ranked	Divided	1	240.243	263.798	1.09805
	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	Squared	Subtracted		31646.1	38288.7	6642.6
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Ranked	Divided	0	8702.94	9169.98	1.05366
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Measured			6452.66	6019.79	1.07191
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Rooted			29.6311	31.1846	1.05243
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Measured		1	20446.1	24136.4	1.18049
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Squared		0	3679.97	3222.25	1.14205
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Rooted		1	51.9812	57.5858	1.10782
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]		Subtracted		120.033	112.905	7.128
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Measured		0	20612.9	20672.6	59.7
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Ranked			13652.7	13061	591.7
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared	Divided	1	32056.4	39965.8	1.24673
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Measured	Subtracted		4916.8	3888.18	1028.62
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Squared		0	99.0201	139.876	40.8559
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Ranked		1	240.788	261.416	20.628
342	40s ribosomal protein s20. [swissprot;acc:p17075]		Divided		243.5	267.21	1.09737

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.