MK5 Microarray Data

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 313 to 362 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
313	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [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). [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). [swissprot;acc:p50579]
316	EIF1	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	242.694	267.017	1.10022
317	no value	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	224.445	204.044	1.09998
318	MRPL3	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	242.011	266.18	1.09987
319	RPL19	60s ribosomal protein l19. [swissprot;acc:p14118]	240.73	264.729	1.09969
320	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	241.892	265.96	1.0995
321	no value	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]		265.959	1.09949
322	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	86.7483	78.8995	1.09948
323	no value	60s ribosomal protein l23a. [swissprot;acc:p29316]	241.884	265.945	1.09947
324	RPS23	40s ribosomal protein s23. [swissprot;acc:p39028]	243.944	268.195	1.09941
325	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
326	RPL5	60s ribosomal protein l5. [swissprot;acc:p46777]	241.899	265.924	1.09932
327	POLR2A	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	243.817	267.962	1.09903
328	DDX24	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	258.437	235.183	1.09888
329	NEUROD2	neurogenic differentiation factor 2 (neurod2). [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). [swissprot;acc:q12873]
331	CDK2AP2	doc-1 related protein (doc-1r). [swissprot;acc:o75956]
332	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]
333	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
334	NEUROD4	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]
335	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
336	CDK2AP1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
337	no value	60s ribosomal protein l12. [swissprot;acc:p30050]	243.583	267.527	1.0983
338		60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]		267.528
339		dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]		267.527
340	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	235.383	258.476	1.09811
341	no value	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	263.798	1.09805
342	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	267.21	1.09737
343	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	265.136	1.0973
344	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
345	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	242.14	265.697	1.09729
346	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]	241.612	265.119
347	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	242.14	265.697
348	no value	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]		265.696	1.09728
349	MED22	surfeit locus protein 5. [swissprot;acc:q15528]
350	SCAPER	zinc finger protein 291. [swissprot;acc:q9by12]
351	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
352	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]
353	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	231.73	211.252	1.09694
354	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691	257.442
355	STX6	syntaxin 6. [swissprot;acc:o43752]	234.673	257.414	1.09691
356	no value	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	266.796	1.09684
357		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	266.661	1.09683
358	RPL10L	ribosomal protein l10-like protein. [refseq;acc:nm_080746]		266.662
359	RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	262.434	1.09678
360	SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	266.559	1.09663
361	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	266.248	1.09644
362	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	231.492	211.136	1.09641

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.