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 2214 to 2263 of 8289 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
1107	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270]	High confidence	204.603	210.324	1.02796
1108	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167]		218.006	212.119	1.02775
	vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]	Low confidence	204.27	199.529	1.02376
1109	mitogen-activated protein kinase 13 (ec 2.7.1.37) (stress-activated protein kinase-4) (mitogen-activated protein kinase p38 delta) (map kinase p38 delta). [swissprot;acc:o15264]		200.443	195.793	1.02375
	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	High confidence	218.098	212.209	1.02775
1110	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161]		216.78	222.782	1.02769
	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]	Low confidence	201.984	197.299	1.02375
1111	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	High confidence	217.99	212.123	1.02766
	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062]	Low confidence	202.004	197.323	1.02372
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	High confidence	251.863	258.829	1.02766
	vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0]	Low confidence	204.256	199.524	1.02372
1113	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]		200.326	195.686	1.02371
	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]	High confidence	251.863	258.829	1.02766
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3. [refseq;acc:nm_032803]	Low confidence	200.679	196.033	1.0237
1115	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]	High confidence	251.863	258.829	1.02766
	low-affinity cationic amino acid transporter-2 (cat-2) (cat2). [swissprot;acc:p52569]	Low confidence	200.679	196.033	1.0237
1116	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]	High confidence	251.863	258.829	1.02766
	pp3111 protein. [refseq;acc:nm_022156]	Low confidence	203.007	198.316	1.02365
1117	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	High confidence	168.989	164.46	1.02754
	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	Low confidence	211.871	216.875	1.02362
1118	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	High confidence	168.995	164.467	1.02753
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Low confidence	187.49	183.168	1.0236
1119	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]		201.761	197.111	1.02359
	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	High confidence	218.528	212.676	1.02752
1120	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]
	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	Low confidence	201.621	196.976	1.02358
1121	rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407]		201.247	196.611
	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050]	High confidence	218.529	212.676	1.02752
1122	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543]	Low confidence	201.537	196.894	1.02358
	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488]	High confidence	218.527	212.676	1.02751
1123	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]		169.031	164.507	1.0275
	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]	Low confidence	201.621	196.976	1.02358
1124	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044]	High confidence	207.553	213.256	1.02748
	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786]	Low confidence	201.395	196.76	1.02356
1125	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	High confidence	204.404	210.022	1.02748
	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	Low confidence	202.352	197.698	1.02354
1126	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	High confidence	218.487	212.656	1.02742
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Low confidence	202.607	197.948	1.02354
1127	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	High confidence	239.219	232.837	1.02741
	proton/amino acid transporter 4. [refseq;acc:nm_152313]	Low confidence	187.77	183.453	1.02353
1128	homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	High confidence	221.286	215.399	1.02733
	ran binding protein ranbp20. [sptrembl;acc:q96qu8]	Low confidence	208.459	203.667	1.02353
1129	homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	High confidence	221.285	215.401	1.02732
	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	Low confidence	202.19	197.541	1.02353
1130	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80]	High confidence	221.285	215.4	1.02732
	single-stranded dna-binding protein mssp-1 (rna binding motif, single- stranded interacting protein 1). [swissprot;acc:p29558]	Low confidence	201.739	197.104	1.02352
1131	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205]		202.3	197.652
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	High confidence	218.484	212.675	1.02731
1132	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]

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.