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 2451 to 2500 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Value Type	red	green	network_comparison	
613	ARD1A	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	Squared	17550.2	20701.1	1.17954	
613	MYCN	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	Rooted	57.1971	61.7626	1.07982	
614	COPB2	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Squared	51527.6	43689.1	1.17942	
614	GABPA	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	Rooted	57.2007	61.7615	1.07973	
614	HOXA10	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Ranked	214.257	202.125	1.06002	
614	SLC4A1AP	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	Measured	11222.2	9948.93	1.12798	
615		ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	Rooted	57.2007	61.7615	1.07973	
615	CKS2	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Measured	11222.2	9948.93	1.12798	
615	COPG	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	Squared	51527.6	43689.1	1.17942	
615	HOXB9	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Ranked	214.257	202.132	1.05999	
616	COPZ1	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	Squared	51527.6	43689.1	1.17942	
616	CTNNAL1	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Measured	11222.2	9948.93	1.12798	
616	HOXA9	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Ranked	214.257	202.132	1.05999	
616	NDUFS8	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	Rooted	57.2007	61.7615	1.07973	
617	ARCN1	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	Squared	51527.6	43689.1	1.17942	
617	DYNC1I1	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Measured	5162.52	5822.47	1.12783	
617	ELOVL1	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	Rooted	57.2008	61.7614	1.07973	
617	HOXC9	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Ranked	214.257	202.135	1.05997	
618	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Ranked	214.256	202.139	1.05994	
618	MYC	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	Rooted	57.208	61.7592	1.07956	
618	NME3	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Measured	7878.27	8879.08	1.12703	
618	PPIE	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	Squared	51527.6	43689.1	1.17942	
619	COPZ2	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Squared	51527.6	43689.1	1.17942	
619	EIF3M	dendritic cell protein. [source:refseq;acc:nm_006360]	Rooted	63.847	68.8873	1.07894	
619	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	Ranked	214.256	202.139	1.05994	
619	NOL5A	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	Measured	3879.99	4371.24	1.12661	
620	CPXM2	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	Rooted	63.847	68.8873	1.07894	
620	FTH1	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	Measured	6227.87	7012.9	1.12605	
620	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	Ranked	214.256	202.14	1.05994	
620	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Squared	32208.8	37986.6	1.17939	
621	CPN1	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	Rooted	63.847	68.8873	1.07894	
621	FTSJ3	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Measured	4115.39	4633.96	1.12601	
621	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	Ranked	214.256	202.14	1.05994	
621	NDUFA6	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	Squared	32193.3	37967.7	1.17937	
622	CPZ	cpz gene product. [source:refseq;acc:nm_003652]	Rooted	63.847	68.8873	1.07894	
622	FTMT	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	Measured	6228.42	7013.21	1.126	
622	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	Ranked	214.256	202.14	1.05994	
622	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Squared	32192.5	37966.8	1.17937	
623	CPE	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	Rooted	63.847	68.8873	1.07894	
623	CREG2	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	Measured	6228.39	7013.19	1.126	
623	GABRG2	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	Ranked	214.256	202.14	1.05994	
623	PDXDC1	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	Squared	32193.3	37967.7	1.17937	
624		dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Measured	6228.39	7013.19	1.126	
624		interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	Ranked	214.256	202.139	1.05994	
624	CPXM1	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	Rooted	63.847	68.8873	1.07894	
624	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	Squared	32192.5	37966.8	1.17937	
625	DLGAP1	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	Measured	6228.39	7013.19	1.126	
625	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	Ranked	214.256	202.14	1.05994	
625	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	Squared	32192.6	37966.9	1.17937	
625	HTRA2	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Rooted	59.6678	64.3767	1.07892	

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/