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

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 294 to 343 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
294	BCCIP	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	240.782	265.717	1.10356
295	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	223.273	202.423	1.103
296	MRPL4	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	241.282	266.12	1.10294
297	no value	60s ribosomal protein l7. [swissprot;acc:p18124]	235.727	259.984	1.1029
298	CAPN2	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	268.632	243.588	1.10281
299	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	268.635	243.592
300	PITRM1	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	150.959	166.351	1.10196
301	ALG1	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	150.982	166.372	1.10193
302	RPL26	60s ribosomal protein l26. [swissprot;acc:q02877]	242.326	267.008	1.10185
303	RPL35	60s ribosomal protein l35. [swissprot;acc:p42766]	242.333	266.999	1.10179
304	no value	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	242.339	266.986	1.1017
305	MRPL2	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]
306	no value	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	242.153	266.673	1.10126
307	SRR	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]
308	RPL34	60s ribosomal protein l34. [swissprot;acc:p49207]
309	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
310	SEC61A1	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]
311	EIF1B	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	242.627	267.151	1.10108
312	RPL3L	60s ribosomal protein l3-like. [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. [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

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.