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

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Showing element 854 to 903 of 3228 in total

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

Hugo	Rank	description	red	green	network_comparison
CPXM2	714	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	223.121	211.685	1.05402
CPZ	716	cpz gene product. [refseq;acc:nm_003652]
CRAT	1698	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]	217.624	214.69	1.01367
CRBN	2564	protein x 0001. [refseq;acc:nm_016302]	208.429	208.779	1.00168
CREB5	1363	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	218.591	213.899	1.02194
CREBL1	1680	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]	216.899	213.889	1.01407
CREBL2	3078	camp responsive element binding protein-like 2. [refseq;acc:nm_001310]	0.00001	0.00001	1
CREG1	705	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	220.438	209.118	1.05413
CREG2	699	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]
CRIM1	1531	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	217.025	213.304	1.01744
CRIPT	3034	postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171]	0.00001	0.00001	1
CRISP1	3018	cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107]
CRISP2	3021	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]
CRISP3	3150	cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108]
CRK	547	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	207.26	194.346	1.06645
CRKL	552	crk-like protein. [swissprot;acc:p46109]
CRNKL1	564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	220.744	207.121	1.06577
CROT	1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	217.523	210.648	1.03264
CRX	1519	cone-rod homeobox protein. [swissprot;acc:o43186]	244.331	240.061	1.01779
CRYAA	2875	alpha crystallin a chain. [swissprot;acc:p02489]	0.00001	0.00001	1
CRYAB	3082	alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]
CSDA	2684	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]	208.438	208.635	1.00095
CSDE1	828	unr protein. [swissprot;acc:o75534]	230.087	220.579	1.0431
CSE1L	1459	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	192.336	188.637	1.01961
CSMD1	1326	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	218.509	213.648	1.02275
CSNK1A1	1496	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]	229.459	225.237	1.01874
CSNK1A1L	1495	casein kinase i alpha s-like. [refseq;acc:nm_145203]
CSNK1D	1721	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	227.125	224.164	1.01321
CSNK1G1	2830	casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0]	0.00001	0.00001	1
CSNK1G2	2986	casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368]
CSNK1G3	2901	casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4]
CSNK2A1P	863	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	240.194	230.957	1.03999
CSNK2A2	864	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
CSRP1	230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	239.35	267.915	1.11934
CSRP2	232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	239.336	267.879	1.11926
CSRP3	233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	239.32	267.842	1.11918
CSTF1	3129	cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]	0.00001	0.00001	1
CSTF2	2140	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	161.547	162.665	1.00692
CSTF2T	2250	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	164.064	165.058	1.00606
CSTF3	1089	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	121.428	125.004	1.02945
CTBP1	1554	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	196.215	193.018	1.01656
CTBP2	1558	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	196.171	192.977	1.01655
CTGF	3040	connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279]	0.00001	0.00001	1
CTH	121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	269.254	327.655	1.2169
CTNNAL1	1834	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]	180.409	182.459	1.01136
CTNNB1	801	beta-catenin (pro2286). [swissprot;acc:p35222]	224.445	214.894	1.04445
CTPS	1755	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	180.609	178.393	1.01242
CTPS2	1757	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	180.537	178.325	1.0124
CTRL	2009	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306]	216.201	214.245	1.00913
CTSB	1667	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	214.898	211.898	1.01416

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.