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	Value Type	Gene	description	Rank	Filtered	Interaction Map	network_comparison	red	green

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Showing element 2558 to 2607 of 3228 in total

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

description	Rank	network_comparison	red	green
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	204	1.13516	201.515	228.752
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	363	1.09639	231.481	211.131
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	588	1.06375	216.557	230.362
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	2695	1.00075	215.545	215.384
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	866	1.03994	221.306	212.806
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	450	1.07815	235.94	218.837
	458	1.07764	235.922	218.925
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	1208	1.02524	224.878	219.342
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	1315	1.02326	222.574	227.752
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	1313		222.573	227.75
signal transducer and activator of transcription 4. [swissprot;acc:q14765]	1314			227.751
signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	1318	1.02304	222.546	227.673
signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	1320	1.02302	222.544	227.667
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	1316	1.02323	222.569	227.739
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	2393	1.00382	182.266	182.962
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	2406	1.00366	182.563	183.232
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	761	1.0493	213.325	203.303
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	2164	1.00673	215.925	214.481
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]	2628	1.00135	224.891	225.195
similar to cg5057 gene product. [sptrembl;acc:q9btt4]	2984	1	0.00001	0.00001
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	1908	1.01034	191.415	193.394
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	1436	1.02022	218.829	214.493
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	631	1.05993	214.256	202.141
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428]	1813	1.01168	216.854	214.35
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	2671	1.00102	216.288	216.067
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	2071	1.0081	217.555	215.807
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2]	1750	1.01264	216.27	213.57
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	3032	1	0.00001	0.00001
similar to mob-lak. [refseq;acc:nm_145279]	2937
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	803	1.04425	212.386	221.785
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557]	1957	1.00978	211.633	213.703
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	1090	1.02945	226.218	232.88
similar to trna synthetase class ii. [refseq;acc:nm_152268]	2714	1.00056	220.224	220.348
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	1086	1.02958	236.679	243.679
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	1454	1.01964	207.024	211.089
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864]	2207	1.00645	199.129	200.413
single-minded homolog 1. [swissprot;acc:p81133]	675	1.05664	226.497	214.355
sipl protein. [refseq;acc:nm_018269]	2247	1.00609	208.609	207.346
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]	2731	1.0003	212.922	212.985
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	935	1.03611	232.473	224.372
skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351]	3037	1	0.00001	0.00001
skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]	2994
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	1198	1.02546	269.59	276.454
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	1195	1.02554	269.608	276.493
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]	2332	1.00452	229.258	230.294
small edrk-rich factor 2. [refseq;acc:nm_005770]	2947	1	0.00001	0.00001
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	2637	1.00126	187.075	186.84
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	2748	1.00017	189.563	189.531
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	891	1.03907	212.028	204.055
small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648]	3004	1	0.00001	0.00001

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.