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

Results: HTML CSV LaTeX

Showing element 2564 to 2613 of 3228 in total

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

Rank	description	red	green	network_comparison
2564	protein x 0001. [refseq;acc:nm_016302]	208.429	208.779	1.00168
2565	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]
2566	serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4]	219.907	220.267	1.00164
2567	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]
2568	serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9]
2569	serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965]
2570	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
2571	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	209.549	209.205
2572	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	203.953	204.285	1.00163
2573	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162]	213.347	213.005	1.00161
2574	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	220.016	219.667	1.00159
2575	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	209.583	209.255	1.00157
2576	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	213.422	213.75	1.00154
2577	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	192.625	192.922
2578	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]	213.422	213.75
2579	nitrilase 1. [refseq;acc:nm_005600]
2580	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
2581	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	213.428	213.756
2582	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]	213.422	213.75
2583	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	213.415	213.743
2584	dystrophin. [swissprot;acc:p11532]	213.422	213.75
2585	angiomotin. [refseq;acc:nm_133265]
2586	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
2587	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]
2588	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	222.305	222.64	1.00151
2589	membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792]	212.74	212.422	1.0015
2590	proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062]	214.605	214.287	1.00148
2591	polybromo 1. [refseq;acc:nm_018165]	220.02	219.696	1.00147
2592	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]
2593	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]
2594	possible global transcription activator snf2l1. [swissprot;acc:p28370]
2595	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]
2596	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]
2597	ran binding protein 11. [refseq;acc:nm_016338]	212.711	212.401	1.00146
2598	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	202.142	202.436	1.00145
2599	ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	211.662	211.361	1.00142
2600	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	224.877	225.193	1.00141
2601	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	214.502	214.2
2602	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	224.875	225.192
2603	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	214.494	214.192
2604	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	214.486	214.184
2605	tcd37 homolog; prune. [refseq;acc:nm_021222]	214.495	214.193
2606	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	214.5	214.198
2607	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	215.497	215.799	1.0014
2608	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
2609	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]
2610	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]
2611	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]
2612	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]
2613	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]

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.