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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 294 to 343 of 3228 in total

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

Rank	Hugo	description	red	network_comparison	green
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	1.10356	265.717
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	1.103	202.423
296	MRPL4	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	241.282	1.10294	266.12
297	no value	60s ribosomal protein l7. [swissprot;acc:p18124]	235.727	1.1029	259.984
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	1.10281	243.588
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	1.10196	166.351
301	ALG1	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	150.982	1.10193	166.372
302	RPL26	60s ribosomal protein l26. [swissprot;acc:q02877]	242.326	1.10185	267.008
303	RPL35	60s ribosomal protein l35. [swissprot;acc:p42766]	242.333	1.10179	266.999
304	no value	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	242.339	1.1017	266.986
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	1.10126	266.673
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	1.10108	267.151
312	RPL3L	60s ribosomal protein l3-like. [swissprot;acc:q92901]	242.195	1.10103	266.663
313	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	232.473	1.10069	211.207
314	METAP1	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	244.126	1.10027	268.604
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	1.10022	267.017
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	1.09998	204.044
318	MRPL3	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	242.011	1.09987	266.18
319	RPL19	60s ribosomal protein l19. [swissprot;acc:p14118]	240.73	1.09969	264.729
320	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	241.892	1.0995	265.96
321	no value	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]		1.09949	265.959
322	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	86.7483	1.09948	78.8995
323	no value	60s ribosomal protein l23a. [swissprot;acc:p29316]	241.884	1.09947	265.945
324	RPS23	40s ribosomal protein s23. [swissprot;acc:p39028]	243.944	1.09941	268.195
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	1.09932	265.924
327	POLR2A	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	243.817	1.09903	267.962
328	DDX24	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	258.437	1.09888	235.183
329	NEUROD2	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	312	1.09859	284
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	1.0983	267.527
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	1.09811	258.476
341	no value	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	1.09805	263.798
342	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	1.09737	267.21
343	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	1.0973	265.136

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.