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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 308 to 357 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
308	RPL34	60s ribosomal protein l34. [source:swissprot;acc:p49207]	242.153	266.673	1.10126	
309	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	242.153	266.673	1.10126	
310	SEC61A1	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	242.153	266.673	1.10126	
311	EIF1B	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	242.627	267.151	1.10108	
312	RPL3L	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	242.195	266.663	1.10103	
313	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	232.473	211.207	1.10069	
314	METAP1	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	244.126	268.604	1.10027	
315	METAP2	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	244.126	268.604	1.10027	
316	EIF1	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	242.694	267.017	1.10022	
317		splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	224.445	204.044	1.09998	
318	MRPL3	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	242.011	266.18	1.09987	
319	RPL19	60s ribosomal protein l19. [source:swissprot;acc:p14118]	240.73	264.729	1.09969	
320	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	241.892	265.96	1.0995	
321		c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	241.892	265.959	1.09949	
322	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	86.7483	78.8995	1.09948	
323		60s ribosomal protein l23a. [source:swissprot;acc:p29316]	241.884	265.945	1.09947	
324	RPS23	40s ribosomal protein s23. [source:swissprot;acc:p39028]	243.944	268.195	1.09941	
325	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	243.944	268.195	1.09941	
326	RPL5	60s ribosomal protein l5. [source:swissprot;acc:p46777]	241.899	265.924	1.09932	
327	POLR2A	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	243.817	267.962	1.09903	
328	DDX24	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	258.437	235.183	1.09888	
329	NEUROD2	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	312	284	1.09859	
330	CHD3	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	312	284	1.09859	
331	CDK2AP2	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	312	284	1.09859	
332	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	312	284	1.09859	
333	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	312	284	1.09859	
334	NEUROD4	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	312	284	1.09859	
335	CHD5	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	312	284	1.09859	
336	CDK2AP1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	312	284	1.09859	
337		60s ribosomal protein l12. [source:swissprot;acc:p30050]	243.583	267.527	1.0983	
338		60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	243.583	267.528	1.0983	
339		dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	243.583	267.527	1.0983	
340	MYEF2	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	235.383	258.476	1.09811	
341		60s ribosomal protein l9. [source:swissprot;acc:p32969]	240.243	263.798	1.09805	
342	RPS20	40s ribosomal protein s20. [source:swissprot;acc:p17075]	243.5	267.21	1.09737	
343	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	241.625	265.136	1.0973	
344		40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	241.625	265.136	1.0973	
345	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	242.14	265.697	1.09729	
346	RPS3	40s ribosomal protein s3. [source:swissprot;acc:p23396]	241.612	265.119	1.09729	
347	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	242.14	265.697	1.09729	
348		adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	242.14	265.696	1.09728	
349	MED22	surfeit locus protein 5. [source:swissprot;acc:q15528]	242.14	265.696	1.09728	
350	SCAPER	zinc finger protein 291. [source:swissprot;acc:q9by12]	242.14	265.696	1.09728	
351	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	242.14	265.696	1.09728	
352	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	242.14	265.696	1.09728	
353	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	231.73	211.252	1.09694	
354	STX10	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	234.691	257.442	1.09694	
355	STX6	syntaxin 6. [source:swissprot;acc:o43752]	234.673	257.414	1.09691	
356		60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	243.24	266.796	1.09684	
357		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	243.12	266.661	1.09683	

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/