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

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Showing element 2530 to 2579 of 3228 in total

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

description	Rank	red	green	network_comparison
serpin b11. [swissprot;acc:q96p15]	795	224.244	234.511	1.04578
serpin b12. [swissprot;acc:q96p63]	2413	218.2	218.984	1.00359
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]	2118	214.632	213.14	1.007
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]	2117
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5]	1290	218.368	213.22	1.02414
sestrin 2 (hi95). [swissprot;acc:p58004]	1279		213.219	1.02415
sestrin 3. [swissprot;acc:p58005]	1278
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	417	233.539	253.197	1.08417
set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]	3039	0.00001	0.00001	1
seven in absentia homolog 1. [refseq;acc:nm_003031]	2234	223.608	225.005	1.00625
seven in absentia homolog 2. [refseq;acc:nm_005067]	2256	223.546	224.869	1.00592
sex comb on midleg homolog 1. [refseq;acc:nm_012236]	3217	0.00001	0.00001	1
sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089]	3120
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137]	1684	216.899	213.889	1.01407
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]	1682
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	1004	238.725	231.059	1.03318
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]	228	226.411	202.088	1.12036
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	2794	0.00001	0.00001	1
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	2867
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	2050	218.79	216.981	1.00834
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	2058
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]	2056
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	1718	206.251	203.553	1.01325
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	1716	206.522	203.818	1.01327
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	1713	206.823	204.111	1.01329
shc transforming protein. [swissprot;acc:p29353]	2125	221.248	222.788	1.00696
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	646	216.731	229.549	1.05914
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	202	201.478	228.784	1.13553
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	204	201.515	228.752	1.13516
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	363	231.481	211.131	1.09639
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	588	216.557	230.362	1.06375
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	2695	215.545	215.384	1.00075
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	866	221.306	212.806	1.03994
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	450	235.94	218.837	1.07815
	458	235.922	218.925	1.07764
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	1208	224.878	219.342	1.02524
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	1315	222.574	227.752	1.02326
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	222.546	227.673	1.02304
signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	1320	222.544	227.667	1.02302
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	1316	222.569	227.739	1.02323
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	2393	182.266	182.962	1.00382
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	2406	182.563	183.232	1.00366
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	761	213.325	203.303	1.0493
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	2164	215.925	214.481	1.00673
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]	2628	224.891	225.195	1.00135
similar to cg5057 gene product. [sptrembl;acc:q9btt4]	2984	0.00001	0.00001	1
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	1908	191.415	193.394	1.01034
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	1436	218.829	214.493	1.02022

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.