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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1025 to 1074 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
257	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	Subtracted	High confidence	242.14	265.697	23.557	
257	DDOST	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Divided	High confidence	200.691	179.88	1.11569	
257	JAG2	jagged 2 precursor (jagged2) (hj2). [source:swissprot;acc:q9y219]	Subtracted	Low confidence	218.715	209.71	9.005	
257	TPM3	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [source:swissprot;acc:p06753]	Divided	Low confidence	201.316	192.404	1.04632	
258	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	Subtracted	High confidence	242.14	265.697	23.557	
258	JAG1	jagged 1 precursor (jagged1) (hj1). [source:swissprot;acc:p78504]	Subtracted	Low confidence	218.714	209.709	9.005	
258	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Divided	High confidence	227.999	204.366	1.11564	
258	TPM1	tropomyosin 1 alpha chain (alpha-tropomyosin). [source:swissprot;acc:p09493]	Divided	Low confidence	201.304	192.427	1.04613	
259		adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Subtracted	High confidence	242.14	265.696	23.556	
259	MEF2C	myocyte-specific enhancer factor 2c. [source:swissprot;acc:q06413]	Subtracted	Low confidence	218.714	209.709	9.005	
259	PDSS1	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	Divided	Low confidence	211.794	202.482	1.04599	
259	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Divided	High confidence	227.999	204.37	1.11562	
260	ANKRD7	ankyrin repeat domain protein 7 (testis-specific protein tsa806). [source:swissprot;acc:q92527]	Divided	Low confidence	216.855	207.34	1.04589	
260	HS3ST6	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Divided	High confidence	219.421	196.978	1.11394	
260	MED22	surfeit locus protein 5. [source:swissprot;acc:q15528]	Subtracted	High confidence	242.14	265.696	23.556	
260	MEF2A	myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [source:swissprot;acc:q02078]	Subtracted	Low confidence	218.715	209.71	9.005	
261	ANKRD19	ba526d8.2 (novel protein similar to kiaa1074). [source:sptrembl;acc:q9h560]	Divided	Low confidence	216.845	207.333	1.04588	
261	HS3ST3A1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Divided	High confidence	219.421	196.978	1.11394	
261	MEF2D	myocyte-specific enhancer factor 2d. [source:swissprot;acc:q14814]	Subtracted	Low confidence	218.713	209.709	9.004	
261	SCAPER	zinc finger protein 291. [source:swissprot;acc:q9by12]	Subtracted	High confidence	242.14	265.696	23.556	
262	ANKRD30A	breast cancer antigen ny-br-1. [source:refseq;acc:nm_052997]	Divided	Low confidence	216.842	207.332	1.04587	
262	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Divided	High confidence	219.421	196.978	1.11394	
262	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Subtracted	High confidence	242.14	265.696	23.556	
262	RNF10	ring finger protein 10. [source:refseq;acc:nm_014868]	Subtracted	Low confidence	208.437	199.44	8.997	
263		sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [source:swissprot;acc:q92581]	Divided	Low confidence	216.546	207.063	1.0458	
263	HS3ST2	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Divided	High confidence	219.421	196.978	1.11394	
263	SOAT1	sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [source:swissprot;acc:p35610]	Subtracted	Low confidence	208.436	199.44	8.996	
263	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Subtracted	High confidence	242.14	265.696	23.556	
264		60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Subtracted	High confidence	243.24	266.796	23.556	
264	ATP2C1	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [source:swissprot;acc:p98194]	Subtracted	Low confidence	218.661	209.669	8.992	
264	DCPS	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Divided	High confidence	219.421	196.978	1.11394	
264	LEO1	senescence downregulated leo1-like. [source:refseq;acc:nm_138792]	Divided	Low confidence	216.546	207.063	1.0458	
265		60s ribosomal protein l9. [source:swissprot;acc:p32969]	Subtracted	High confidence	240.243	263.798	23.555	
265	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Divided	High confidence	225.217	202.459	1.11241	
265	SLC9A7	solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [source:refseq;acc:nm_032591]	Divided	Low confidence	216.546	207.063	1.0458	
265	TNKS2	tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [source:swissprot;acc:q9h2k2]	Subtracted	Low confidence	214.675	205.692	8.983	
266	PHKG2	phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [source:swissprot;acc:p15735]	Subtracted	Low confidence	217.756	226.722	8.966	
266	RPL10L	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Subtracted	High confidence	243.12	266.662	23.542	
266	SIN3A	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Divided	High confidence	241.07	267.88	1.11121	
266	WDR92	calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [source:swissprot;acc:p06705]	Divided	Low confidence	214.887	205.509	1.04563	
267		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Subtracted	High confidence	243.12	266.661	23.541	
267		cln3 protein (battenin) (batten disease protein). [source:swissprot;acc:q13286]	Subtracted	Low confidence	211.912	202.965	8.947	
267	DENR	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Divided	High confidence	241.07	267.88	1.11121	
267	TNS1	tensin. [source:refseq;acc:nm_022648]	Divided	Low confidence	215.258	205.872	1.04559	
268	EIF5	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Divided	High confidence	271.016	244.167	1.10996	
268	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Subtracted	High confidence	241.625	265.136	23.511	
268	SOAT2	sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [source:swissprot;acc:o75908]	Divided	Low confidence	208.469	199.455	1.04519	
268	TPM3	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [source:swissprot;acc:p06753]	Subtracted	Low confidence	201.316	192.404	8.912	
269		40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Subtracted	High confidence	241.625	265.136	23.511	
269	BTBD14B	transcriptional repressor nac1. [source:refseq;acc:nm_052876]	Subtracted	Low confidence	202.309	211.2	8.891	

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/