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

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Showing element 1030 to 1079 of 16578 in total

Value Type	Ranked
Filtered	1

Rank	Hugo	Network Comparison Type	description	Interaction Map	red	green	network_comparison	
258	JAG1	Subtracted	jagged 1 precursor (jagged1) (hj1). [source:swissprot;acc:p78504]	Low confidence	218.714	209.709	9.005	
258	MXD4	Divided	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	High confidence	227.999	204.366	1.11564	
258	TPM1	Divided	tropomyosin 1 alpha chain (alpha-tropomyosin). [source:swissprot;acc:p09493]	Low confidence	201.304	192.427	1.04613	
259		Subtracted	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	High confidence	242.14	265.696	23.556	
259	MEF2C	Subtracted	myocyte-specific enhancer factor 2c. [source:swissprot;acc:q06413]	Low confidence	218.714	209.709	9.005	
259	PDSS1	Divided	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	Low confidence	211.794	202.482	1.04599	
259	RAB24	Divided	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	High confidence	227.999	204.37	1.11562	
260	ANKRD7	Divided	ankyrin repeat domain protein 7 (testis-specific protein tsa806). [source:swissprot;acc:q92527]	Low confidence	216.855	207.34	1.04589	
260	HS3ST6	Divided	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	High confidence	219.421	196.978	1.11394	
260	MED22	Subtracted	surfeit locus protein 5. [source:swissprot;acc:q15528]	High confidence	242.14	265.696	23.556	
260	MEF2A	Subtracted	myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [source:swissprot;acc:q02078]	Low confidence	218.715	209.71	9.005	
261	ANKRD19	Divided	ba526d8.2 (novel protein similar to kiaa1074). [source:sptrembl;acc:q9h560]	Low confidence	216.845	207.333	1.04588	
261	HS3ST3A1	Divided	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	High confidence	219.421	196.978	1.11394	
261	MEF2D	Subtracted	myocyte-specific enhancer factor 2d. [source:swissprot;acc:q14814]	Low confidence	218.713	209.709	9.004	
261	SCAPER	Subtracted	zinc finger protein 291. [source:swissprot;acc:q9by12]	High confidence	242.14	265.696	23.556	
262	ANKRD30A	Divided	breast cancer antigen ny-br-1. [source:refseq;acc:nm_052997]	Low confidence	216.842	207.332	1.04587	
262	HS3ST3B1	Divided	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	High confidence	219.421	196.978	1.11394	
262	PEX1	Subtracted	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	High confidence	242.14	265.696	23.556	
262	RNF10	Subtracted	ring finger protein 10. [source:refseq;acc:nm_014868]	Low confidence	208.437	199.44	8.997	
263		Divided	sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [source:swissprot;acc:q92581]	Low confidence	216.546	207.063	1.0458	
263	HS3ST2	Divided	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	High confidence	219.421	196.978	1.11394	
263	SOAT1	Subtracted	sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [source:swissprot;acc:p35610]	Low confidence	208.436	199.44	8.996	
263	TXNDC9	Subtracted	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	High confidence	242.14	265.696	23.556	
264		Subtracted	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	High confidence	243.24	266.796	23.556	
264	ATP2C1	Subtracted	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]	Low confidence	218.661	209.669	8.992	
264	DCPS	Divided	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	High confidence	219.421	196.978	1.11394	
264	LEO1	Divided	senescence downregulated leo1-like. [source:refseq;acc:nm_138792]	Low confidence	216.546	207.063	1.0458	
265		Subtracted	60s ribosomal protein l9. [source:swissprot;acc:p32969]	High confidence	240.243	263.798	23.555	
265	SF3B1	Divided	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	High confidence	225.217	202.459	1.11241	
265	SLC9A7	Divided	solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [source:refseq;acc:nm_032591]	Low confidence	216.546	207.063	1.0458	
265	TNKS2	Subtracted	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]	Low confidence	214.675	205.692	8.983	
266	PHKG2	Subtracted	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]	Low confidence	217.756	226.722	8.966	
266	RPL10L	Subtracted	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	High confidence	243.12	266.662	23.542	
266	SIN3A	Divided	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	High confidence	241.07	267.88	1.11121	
266	WDR92	Divided	calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [source:swissprot;acc:p06705]	Low confidence	214.887	205.509	1.04563	
267		Subtracted	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	High confidence	243.12	266.661	23.541	
267		Subtracted	cln3 protein (battenin) (batten disease protein). [source:swissprot;acc:q13286]	Low confidence	211.912	202.965	8.947	
267	DENR	Divided	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	High confidence	241.07	267.88	1.11121	
267	TNS1	Divided	tensin. [source:refseq;acc:nm_022648]	Low confidence	215.258	205.872	1.04559	
268	EIF5	Divided	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	High confidence	271.016	244.167	1.10996	
268	PRMT3	Subtracted	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	High confidence	241.625	265.136	23.511	
268	SOAT2	Divided	sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [source:swissprot;acc:o75908]	Low confidence	208.469	199.455	1.04519	
268	TPM3	Subtracted	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [source:swissprot;acc:p06753]	Low confidence	201.316	192.404	8.912	
269		Subtracted	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	High confidence	241.625	265.136	23.511	
269	BTBD14B	Subtracted	transcriptional repressor nac1. [source:refseq;acc:nm_052876]	Low confidence	202.309	211.2	8.891	
269	PCYT1A	Divided	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	High confidence	241.373	267.352	1.10763	
269	SOAT1	Divided	sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [source:swissprot;acc:p35610]	Low confidence	208.436	199.44	1.04511	
270	FLAD1	Divided	fad synthetase. [source:refseq;acc:nm_025207]	High confidence	241.373	267.352	1.10763	
270	KHDRBS3	Subtracted	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Low confidence	209.532	200.653	8.879	
270	RNF10	Divided	ring finger protein 10. [source:refseq;acc:nm_014868]	Low confidence	208.437	199.44	1.04511	

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/