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

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Showing element 2630 to 2679 of 3228 in total

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

description	Rank	red	green	network_comparison
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]	1182	4392.63	4776.19	1.08732
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]	1179
solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	2965	0.00001	0.00001	1
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]	1817	5633.44	5997	1.06454
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]	1831
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	2317	6961.44	7274.17	1.04492
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]	2315	6961.11	7273.85	1.04493
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	2311	6961.19	7273.93
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	2496	5534.46	5684.97	1.0272
solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483]	3026	0.00001	0.00001	1
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	614	11222.2	9948.93	1.12798
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	1166	6606.3	7185.01	1.0876
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	1928	7514.8	7980.22	1.06193
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	1905	7497.96	7967.09	1.06257
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]	95	2397.19	3343.62	1.39481
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	442	6251.99	7192.17	1.15038
sorting nexin 1. [swissprot;acc:q13596]	2536	5932.05	6071.35	1.02348
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	1972	4374.32	4126.96	1.05994
sorting nexin 16. [swissprot;acc:p57768]	3108	0.00001	0.00001	1
sorting nexin 17. [swissprot;acc:q15036]	2551	4725.79	4824.4	1.02087
sorting nexin 5. [swissprot;acc:q9y5x3]	2741	5339.67	5327.2	1.00234
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	2657	5327.58	5371.47	1.00824
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	1049	4757.46	5198.91	1.09279
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	188	4571.89	5864.86	1.28281
sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486]	3062	0.00001	0.00001	1
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
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	3038
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082]	1602	5232.14	5605.8	1.07142
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020]	1601
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	968	7813.48	8570.11	1.09684
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470]	1334	5804.75	6270.15	1.08018
sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280]	2797	0.00001	0.00001	1
spermatogenesis associated 6. [refseq;acc:nm_019073]	69	6475.5	10307.5	1.59177
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]	1306	5500.92	5949.26	1.0815
spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788]	3118	0.00001	0.00001	1
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]	1238	5873.56	6370.31	1.08457
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	7	1153.5	339.5	3.39764
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	472	9649.61	11053.5	1.14549
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	485
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	1468	5473.09	5887.45	1.07571
spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	2879	0.00001	0.00001	1
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	236	4723.53	5828.46	1.23392
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333]	1958	5448.35	5777.35	1.06039
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	649	5248.07	5901.72	1.12455
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	296	4911.81	5909.18	1.20306
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	648	5248.07	5901.72	1.12455
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	191	4638.1	5923.4	1.27712
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	348	4991.02	5885.09	1.17914

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.