Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Network Comparison Type Value Type description Filtered Interaction Map network_comparison green red
Results: HTML CSV LaTeX Showing element 2563 to 2612 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Filtered	1
Interaction Map	High confidence

Rank	description	network_comparison	green	red	
2563	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [source:swissprot;acc:p55263]	1.00168	208.779	208.429	
2564	protein x 0001. [source:refseq;acc:nm_016302]	1.00168	208.779	208.429	
2565	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	1.00168	208.779	208.429	
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). [source:swissprot;acc:q96gd4]	1.00164	220.267	219.907	
2567	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [source:swissprot;acc:q02241]	1.00164	220.267	219.907	
2568	serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [source:swissprot;acc:q9uqb9]	1.00164	220.267	219.907	
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). [source:swissprot;acc:o14965]	1.00164	220.267	219.907	
2570	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247]	1.00164	220.267	219.907	
2571	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	1.00164	209.205	209.549	
2572	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [source:swissprot;acc:q16514]	1.00163	204.285	203.953	
2573	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [source:swissprot;acc:q13162]	1.00161	213.005	213.347	
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. [source:refseq;acc:nm_003074]	1.00159	219.667	220.016	
2575	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [source:swissprot;acc:p17706]	1.00157	209.255	209.583	
2576	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [source:swissprot;acc:q13884]	1.00154	213.75	213.422	
2577	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	1.00154	192.922	192.625	
2578	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [source:swissprot;acc:q13425]	1.00154	213.75	213.422	
2579	nitrilase 1. [source:refseq;acc:nm_005600]	1.00154	213.75	213.422	
2580	utrophin (dystrophin-related protein 1) (drp1) (drp). [source:swissprot;acc:p46939]	1.00154	213.75	213.422	
2581	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [source:swissprot;acc:o60941]	1.00154	213.756	213.428	
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). [source:swissprot;acc:p11182]	1.00154	213.75	213.422	
2583	dystrobrevin alpha (dystrobrevin-alpha). [source:swissprot;acc:q9y4j8]	1.00154	213.743	213.415	
2584	dystrophin. [source:swissprot;acc:p11532]	1.00154	213.75	213.422	
2585	angiomotin. [source:refseq;acc:nm_133265]	1.00154	213.75	213.422	
2586	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [source:refseq;acc:nm_016201]	1.00154	213.75	213.422	
2587	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [source:swissprot;acc:q13424]	1.00154	213.75	213.422	
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). [source:swissprot;acc:p10809]	1.00151	222.64	222.305	
2589	membrane protein expressed in epithelial-like lung adenocarcinoma. [source:refseq;acc:nm_024792]	1.0015	212.422	212.74	
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). [source:swissprot;acc:p34062]	1.00148	214.287	214.605	
2591	polybromo 1. [source:refseq;acc:nm_018165]	1.00147	219.696	220.02	
2592	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [source:refseq;acc:nm_003601]	1.00147	219.696	220.02	
2593	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [source:swissprot;acc:p51532]	1.00147	219.696	220.02	
2594	possible global transcription activator snf2l1. [source:swissprot;acc:p28370]	1.00147	219.696	220.02	
2595	tbp-associated factor 172 (taf-172) (taf(ii)170). [source:swissprot;acc:o14981]	1.00147	219.696	220.02	
2596	possible global transcription activator snf2l2 (snf2-alpha). [source:swissprot;acc:p51531]	1.00147	219.696	220.02	
2597	ran binding protein 11. [source:refseq;acc:nm_016338]	1.00146	212.401	212.711	
2598	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [source:swissprot;acc:q15542]	1.00145	202.436	202.142	
2599	ba207c16.2 (fragment). [source:sptrembl;acc:q9nql7]	1.00142	211.361	211.662	
2600	interferon-related developmental regulator 2 (skmc15 protein). [source:swissprot;acc:q12894]	1.00141	225.193	224.877	
2601	cyclin m3; ancient conserved domain protein 3. [source:refseq;acc:nm_017623]	1.00141	214.2	214.502	
2602	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [source:swissprot;acc:o15511]	1.00141	225.192	224.875	
2603	cyclin m4; ancient conserved domain protein 4. [source:refseq;acc:nm_020184]	1.00141	214.192	214.494	
2604	cyclin m2; ancient conserved domain protein 2. [source:refseq;acc:nm_017649]	1.00141	214.184	214.486	
2605	tcd37 homolog; prune. [source:refseq;acc:nm_021222]	1.00141	214.193	214.495	
2606	cyclin m1; ancient conserved domain protein 1. [source:refseq;acc:nm_020348]	1.00141	214.198	214.5	
2607	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	1.0014	215.799	215.497	
2608	nefa-interacting nuclear protein nip30. [source:refseq;acc:nm_024946]	1.0014	215.799	215.497	
2609	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [source:swissprot;acc:q8te12]	1.0014	215.799	215.497	
2610	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [source:swissprot;acc:o94826]	1.0014	215.799	215.497	
2611	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [source:swissprot;acc:o60663]	1.0014	215.799	215.497	
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). [source:swissprot;acc:p49721]	1.0014	215.799	215.497	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/