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

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Showing element 180 to 229 of 3228 in total

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

Rank	description	Hugo	red	green	network_comparison
180	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	TARDBP	256.228	298.438	1.16474
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	B9D1	229.818	267.265	1.16294
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	HAT1	277.546	240.461	1.15422
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	NCBP2	228.306	198.011	1.153
184	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	OSR1	274.027	237.79	1.15239
185	adiponectin receptor 2. [refseq;acc:nm_024551]	ADIPOR2	281.582	246.371	1.14292
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]	FLNB	226.582	198.444	1.14179
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	REV1
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	PRMT1
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	PRMT8
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	SNRP70
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	no value
192	musashi 2 isoform a. [refseq;acc:nm_138962]	MSI2	227.491	199.458	1.14055
193	musashi 1. [refseq;acc:nm_002442]	MSI1
194	nuclear protein ukp68. [refseq;acc:nm_024824]	ZC3H14
195	huntingtin interacting protein c. [refseq;acc:nm_012272]	PRPF40B	227.971	200.417	1.13748
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	FOXP4	263.215	231.407	1.13745
197	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	FOXP1
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	FOXP3	263.191	231.394	1.13741
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	EGFL8	242.735	276.059	1.13729
200	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	EGFL7	242.718	276.018	1.1372
201	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	SF4	240.133	211.382	1.13601
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	TRPC4	201.478	228.784	1.13553
203	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	TBC1D10A	201.515	228.752	1.13516
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	TRPC5
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	LUC7L2	228.1	200.968	1.13501
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	LUC7L	228.085	201.006	1.13472
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	PSEN2	285.684	252.234	1.13261
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]	SKP1A
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]	FBXW7
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	CUL2
211	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	PSEN1
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	CUL1
213	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	PLDN	210.693	186.95	1.127
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	LASS2	191.644	170.192	1.12605
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	no value	112	126	1.125
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	MYH4
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	MYH8
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	MYH2
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	MYH3
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	MYH1
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	no value
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	MYH7B
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	MYH13
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	SLC15A2	185.969	165.623	1.12285
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	SNRPD2	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	COMP	239.991	269.238	1.12187
227	thrombospondin 3 precursor. [swissprot;acc:p49746]	THBS3	239.99	269.234	1.12186
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	SH2D3C	226.411	202.088	1.12036
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	BCAR3	226.401	202.094	1.12028

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.