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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 163 to 212 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
163	SNF8	eap30 subunit of ell complex. [refseq;acc:nm_007241]	209.299	249.187	1.19058
164	SLC39A6	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]
165	GAD2	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
166	NAPG	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]
167	GAD1	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]
168	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	82.5916	98.0548	1.18722
169	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]
170	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	227.199	192.715	1.17894
171	TIAL1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	227.202	192.823	1.17829
172	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	174.667	205.556	1.17685
173	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	227.032	193.056	1.17599
174	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	335	286	1.17133
175	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	199.949	234.187	1.17123
176	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	275.754	235.908	1.1689
177	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	229.406	196.695	1.1663
178	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	226.887	194.72	1.1652
179		huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	226.884	194.79	1.16476
180	TARDBP	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	256.228	298.438	1.16474
181	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	229.818	267.265	1.16294
182	HAT1	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	277.546	240.461	1.15422
183	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	228.306	198.011	1.153
184	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	274.027	237.79	1.15239
185	ADIPOR2	adiponectin receptor 2. [refseq;acc:nm_024551]	281.582	246.371	1.14292
186	FLNB	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]	226.582	198.444	1.14179
187	REV1	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
188	PRMT1	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
189	PRMT8	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
190	SNRP70	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
191	no value	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
192	MSI2	musashi 2 isoform a. [refseq;acc:nm_138962]	227.491	199.458	1.14055
193	MSI1	musashi 1. [refseq;acc:nm_002442]
194	ZC3H14	nuclear protein ukp68. [refseq;acc:nm_024824]
195	PRPF40B	huntingtin interacting protein c. [refseq;acc:nm_012272]	227.971	200.417	1.13748
196	FOXP4	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	263.215	231.407	1.13745
197	FOXP1	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]
198	FOXP3	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	263.191	231.394	1.13741
199	EGFL8	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	242.735	276.059	1.13729
200	EGFL7	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	242.718	276.018	1.1372
201	SF4	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	240.133	211.382	1.13601
202	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	201.478	228.784	1.13553
203	TBC1D10A	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	201.515	228.752	1.13516
204	TRPC5	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
205	LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	228.1	200.968	1.13501
206	LUC7L	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	228.085	201.006	1.13472
207	PSEN2	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	285.684	252.234	1.13261
208	SKP1A	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	FBXW7	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	CUL2	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
211	PSEN1	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
212	CUL1	cullin homolog 1 (cul-1). [swissprot;acc:q13616]

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
- Hugo is the HGNC identifier if it exists
- 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.