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

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Showing element 168 to 217 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	green	network_comparison	red
168	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	98.0548	1.18722	82.5916
169	apg3p; pc3-96 protein. [refseq;acc:nm_022488]
170	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	192.715	1.17894	227.199
171	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	192.823	1.17829	227.202
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	205.556	1.17685	174.667
173	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	193.056	1.17599	227.032
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	286	1.17133	335
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	234.187	1.17123	199.949
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	235.908	1.1689	275.754
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	196.695	1.1663	229.406
178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	194.72	1.1652	226.887
179	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	194.79	1.16476	226.884
180	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	298.438	1.16474	256.228
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	267.265	1.16294	229.818
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	240.461	1.15422	277.546
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	198.011	1.153	228.306
184	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	237.79	1.15239	274.027
185	adiponectin receptor 2. [refseq;acc:nm_024551]	246.371	1.14292	281.582
186	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	198.444	1.14179	226.582
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
192	musashi 2 isoform a. [refseq;acc:nm_138962]	199.458	1.14055	227.491
193	musashi 1. [refseq;acc:nm_002442]
194	nuclear protein ukp68. [refseq;acc:nm_024824]
195	huntingtin interacting protein c. [refseq;acc:nm_012272]	200.417	1.13748	227.971
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	231.407	1.13745	263.215
197	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	231.394	1.13741	263.191
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	276.059	1.13729	242.735
200	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	276.018	1.1372	242.718
201	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	211.382	1.13601	240.133
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	228.784	1.13553	201.478
203	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	228.752	1.13516	201.515
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	200.968	1.13501	228.1
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	201.006	1.13472	228.085
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	252.234	1.13261	285.684
208	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
209	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
211	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
213	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	186.95	1.127	210.693
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	170.192	1.12605	191.644
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	126	1.125	112
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]

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.