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 214 to 263 of 3228 in total

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

Rank	description	red	green	network_comparison
214	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	4074.83	5086.49	1.24827
215	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	16074	12888.4	1.24717
216	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	16071.6	12886.8	1.24714
217	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]
218	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	16070.4	12886	1.24712
219	transforming protein n-ras. [swissprot;acc:p01111]	16069.8	12885.6	1.24711
220	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	41482.5	33356.5	1.24361
221	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
222	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
223	cytohesin 4. [swissprot;acc:q9uia0]
224	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
225	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	9035	7279.6	1.24114
226	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
227	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]
228	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
229	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
230	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]
231	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
232	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]
233	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
234	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	5181.2	6410.58	1.23728
235	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
236	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	4723.53	5828.46	1.23392
237	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	4567.04	5631.2	1.23301
238	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	27642.5	22440.4	1.23182
239	carboxypeptidase b precursor. [refseq;acc:nm_020361]	7711.38	6265.8	1.23071
240	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	7711.36	6265.79
241	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	7711.31	6265.76
242	max protein. [swissprot;acc:p25912]	4640.26	5704.87	1.22943
243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	4246.95	5208.98	1.22652
244	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	4250.14	5211.25	1.22614
245	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	4251.65	5212.33	1.22595
246	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	4252.66	5213.05	1.22583
247	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	6416.68	7865.15	1.22574
248	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	6417.18	7859.6	1.22477
249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]		7859.59
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]		7859.6
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]
252	crk-like protein. [swissprot;acc:p46109]
253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]		7859.59
254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]		7859.6
255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
256	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	6417.19	7859.51	1.22476
257	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	6417.31	7858.12	1.22452
258	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	6417.33	7857.93	1.22449
259	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	6417.81	7852.52	1.22355
260	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	4244.95	5193.42	1.22343
261		4247.36	5192.61	1.22255
262	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	24896.4	20431.7	1.21852
263	trs85 homolog. [swissprot;acc:q9y2l5]

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.