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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 2562 to 2611 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
2562	GYG1	glycogenin-1 (ec 2.4.1.186). [source:swissprot;acc:p46976]	208.429	208.779	1.00168	
2563	ADK	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [source:swissprot;acc:p55263]	208.429	208.779	1.00168	
2564	CRBN	protein x 0001. [source:refseq;acc:nm_016302]	208.429	208.779	1.00168	
2565	GYG2	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	208.429	208.779	1.00168	
2566	AURKB	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]	219.907	220.267	1.00164	
2567	KIF23	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [source:swissprot;acc:q02241]	219.907	220.267	1.00164	
2568	AURKC	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]	219.907	220.267	1.00164	
2569	AURKA	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]	219.907	220.267	1.00164	
2570	CYLD	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247]	219.907	220.267	1.00164	
2571		protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	209.549	209.205	1.00164	
2572	TAF12	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [source:swissprot;acc:q16514]	203.953	204.285	1.00163	
2573	PRDX4	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]	213.347	213.005	1.00161	
2574	SMARCC1	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]	220.016	219.667	1.00159	
2575	PTPN2	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [source:swissprot;acc:p17706]	209.583	209.255	1.00157	
2576	SNTB1	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]	213.422	213.75	1.00154	
2577	CANT1	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	192.625	192.922	1.00154	
2578	SNTB2	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [source:swissprot;acc:q13425]	213.422	213.75	1.00154	
2579	NIT1	nitrilase 1. [source:refseq;acc:nm_005600]	213.422	213.75	1.00154	
2580	UTRN	utrophin (dystrophin-related protein 1) (drp1) (drp). [source:swissprot;acc:p46939]	213.422	213.75	1.00154	
2581	DTNB	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [source:swissprot;acc:o60941]	213.428	213.756	1.00154	
2582	DBT	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]	213.422	213.75	1.00154	
2583	DTNA	dystrobrevin alpha (dystrobrevin-alpha). [source:swissprot;acc:q9y4j8]	213.415	213.743	1.00154	
2584		dystrophin. [source:swissprot;acc:p11532]	213.422	213.75	1.00154	
2585	AMOT	angiomotin. [source:refseq;acc:nm_133265]	213.422	213.75	1.00154	
2586	AMOTL2	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [source:refseq;acc:nm_016201]	213.422	213.75	1.00154	
2587	SNTA1	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]	213.422	213.75	1.00154	
2588	HSPD1	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]	222.305	222.64	1.00151	
2589	FAM57A	membrane protein expressed in epithelial-like lung adenocarcinoma. [source:refseq;acc:nm_024792]	212.74	212.422	1.0015	
2590	PSMA6	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]	214.605	214.287	1.00148	
2591	PBRM1	polybromo 1. [source:refseq;acc:nm_018165]	220.02	219.696	1.00147	
2592	SMARCA5	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [source:refseq;acc:nm_003601]	220.02	219.696	1.00147	
2593	SMARCA4	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [source:swissprot;acc:p51532]	220.02	219.696	1.00147	
2594	SMARCA1	possible global transcription activator snf2l1. [source:swissprot;acc:p28370]	220.02	219.696	1.00147	
2595	BTAF1	tbp-associated factor 172 (taf-172) (taf(ii)170). [source:swissprot;acc:o14981]	220.02	219.696	1.00147	
2596	SMARCA2	possible global transcription activator snf2l2 (snf2-alpha). [source:swissprot;acc:p51531]	220.02	219.696	1.00147	
2597	IPO11	ran binding protein 11. [source:refseq;acc:nm_016338]	212.711	212.401	1.00146	
2598	TAF5	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [source:swissprot;acc:q15542]	202.142	202.436	1.00145	
2599	KIAA1432	ba207c16.2 (fragment). [source:sptrembl;acc:q9nql7]	211.662	211.361	1.00142	
2600	HYAL3	interferon-related developmental regulator 2 (skmc15 protein). [source:swissprot;acc:q12894]	224.877	225.193	1.00141	
2601	CNNM3	cyclin m3; ancient conserved domain protein 3. [source:refseq;acc:nm_017623]	214.502	214.2	1.00141	
2602	ARPC5	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [source:swissprot;acc:o15511]	224.875	225.192	1.00141	
2603	CNNM4	cyclin m4; ancient conserved domain protein 4. [source:refseq;acc:nm_020184]	214.494	214.192	1.00141	
2604	CNNM2	cyclin m2; ancient conserved domain protein 2. [source:refseq;acc:nm_017649]	214.486	214.184	1.00141	
2605	PRUNE	tcd37 homolog; prune. [source:refseq;acc:nm_021222]	214.495	214.193	1.00141	
2606	CNNM1	cyclin m1; ancient conserved domain protein 1. [source:refseq;acc:nm_020348]	214.5	214.198	1.00141	
2607	MRPS22	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	215.497	215.799	1.0014	
2608		nefa-interacting nuclear protein nip30. [source:refseq;acc:nm_024946]	215.497	215.799	1.0014	
2609	LMX1A	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [source:swissprot;acc:q8te12]	215.497	215.799	1.0014	
2610	TOMM70A	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [source:swissprot;acc:o94826]	215.497	215.799	1.0014	
2611	LMX1B	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [source:swissprot;acc:o60663]	215.497	215.799	1.0014	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/