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

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Showing element 2608 to 2657 of 3228 in total

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

description	Rank	network_comparison	green	red
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	3012	1	0.00001	0.00001
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	388	1.09015	208.756	227.575
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	389
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	173	1.17599	193.056	227.032
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	225	1.12243	201.769	226.471
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	245	1.11751	202.333	226.109
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]	1346	1.02224	221.594	216.772
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	232	1.11926	267.879	239.336
snare associated protein snapin. [refseq;acc:nm_012437]	1163	1.02632	215.097	220.758
snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966]	2849	1	0.00001	0.00001
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	2000	1.00931	202.739	204.626
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	1996	1.00936	202.784	204.682
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023]	1424	1.02068	219.157	214.717
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	1428
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637]	1427
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	1911	1.01033	215.256	217.48
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]	2456	1.00314	205.326	204.683
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183]	2458
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]	2455
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4]	2454
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3]	2047	1.00838	226.003	224.124
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]	2048
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]	2464	1.00308	235.088	235.812
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749]	2461
solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	2965	1	0.00001	0.00001
solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7]	2120	1.00696	222.788	221.248
solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3]	2138
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	1900	1.01034	193.38	191.401
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]	1907		193.387	191.408
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	1903		193.385	191.406
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	745	1.05072	225.568	214.679
solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483]	3026	1	0.00001	0.00001
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	1832	1.01136	182.459	180.409
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	1999	1.00931	202.748	204.636
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	560	1.06589	193.021	205.74
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	561	1.06578	193.183	205.89
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	131	1.21228	242.562	294.053
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	943	1.03586	205.087	212.442
sorting nexin 1. [swissprot;acc:q13596]	1150	1.02694	215.522	209.868
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	243	1.11785	254.15	227.357
sorting nexin 16. [swissprot;acc:p57768]	3108	1	0.00001	0.00001
sorting nexin 17. [swissprot;acc:q15036]	638	1.05957	242.258	228.639
sorting nexin 5. [swissprot;acc:q9y5x3]	678	1.05609	220.175	208.482
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	778	1.04848	219.332	209.191
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	2335	1.00452	230.294	229.258
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	254	1.11569	179.88	200.691
sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486]	3062	1	0.00001	0.00001
sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515]	2899
spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087]	2987
speckle-type poz protein. [swissprot;acc:o43791]	3031

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.