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

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Showing element 451 to 500 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
226	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Subtracted	6417.31	7858.12	1440.81
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Divided	9035	7279.6	1.24114
227	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Subtracted	6417.33	7857.93	1440.6
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Divided	9035	7279.6	1.24114
228	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Subtracted	6417.81	7852.52	1434.71
229	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Divided	9035	7279.6	1.24114
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Subtracted	10434.4	11846.2	1411.8
230	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]		9649.61	11053.5	1403.89
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided	9035	7279.6	1.24114
231	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	Subtracted	9649.61	11053.5	1403.89
232	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Divided	9035	7279.6	1.24114
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	Subtracted	9649.61	11053.5	1403.89
233	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Divided	9035	7279.6	1.24114
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Subtracted	9649.61	11053.5	1403.89
234	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Divided	5181.2	6410.58	1.23728
235	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Subtracted	9649.61	11053.5	1403.89
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Divided	5181.2	6410.58	1.23728
236	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Subtracted	9649.61	11053.5	1403.89
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Divided	4723.53	5828.46	1.23392
237	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Subtracted	9649.61	11053.5	1403.89
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Divided	4567.04	5631.2	1.23301
238	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]		27642.5	22440.4	1.23182
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Subtracted	9649.61	11053.5	1403.89
239	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Divided	7711.38	6265.8	1.23071
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	Subtracted	9649.61	11053.5	1403.89
240	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Divided	7711.36	6265.79	1.23071
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Subtracted	9649.61	11053.5	1403.89
241	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Divided	7711.31	6265.76	1.23071
242	max protein. [swissprot;acc:p25912]		4640.26	5704.87	1.22943
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Subtracted	9649.61	11053.5	1403.89
243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Divided	4246.95	5208.98	1.22652
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Subtracted	9649.61	11053.5	1403.89
244	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Divided	4250.14	5211.25	1.22614
245	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]		4251.65	5212.33	1.22595
	methyltransferase like 2. [refseq;acc:nm_018396]	Subtracted	13241.4	11864	1377.4
246	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Divided	4252.66	5213.05	1.22583
247	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Subtracted	13241.4	11864	1377.4
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	Divided	6416.68	7865.15	1.22574
248	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Subtracted	13241.4	11864	1377.4
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Divided	6417.18	7859.6	1.22477
249	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Subtracted	4405.4	5782.08	1376.68
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Divided	6417.18	7859.59	1.22477
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]			7859.6
	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]	Subtracted	4578.09	5939.91	1361.82

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.