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 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	description	red	green	network_comparison	
294	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [source:refseq;acc:nm_016567]	240.782	265.717	1.10356	
295	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	223.273	202.423	1.103	
296	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	241.282	266.12	1.10294	
297	60s ribosomal protein l7. [source:swissprot;acc:p18124]	235.727	259.984	1.1029	
298	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). [source:swissprot;acc:p17655]	268.632	243.588	1.10281	
299	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	268.635	243.592	1.10281	
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	150.959	166.351	1.10196	
301	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	150.982	166.372	1.10193	
302	60s ribosomal protein l26. [source:swissprot;acc:q02877]	242.326	267.008	1.10185	
303	60s ribosomal protein l35. [source:swissprot;acc:p42766]	242.333	266.999	1.10179	
304	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	242.339	266.986	1.1017	
305	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	242.339	266.986	1.1017	
306	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	242.153	266.673	1.10126	
307	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	242.153	266.673	1.10126	
308	60s ribosomal protein l34. [source:swissprot;acc:p49207]	242.153	266.673	1.10126	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	242.153	266.673	1.10126	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	242.153	266.673	1.10126	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	242.627	267.151	1.10108	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	242.195	266.663	1.10103	
313	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	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	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	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	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	242.011	266.18	1.09987	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	240.73	264.729	1.09969	
320	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	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	40s ribosomal protein s23. [source:swissprot;acc:p39028]	243.944	268.195	1.09941	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	243.944	268.195	1.09941	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	241.899	265.924	1.09932	
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	243.817	267.962	1.09903	
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	258.437	235.183	1.09888	
329	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	312	284	1.09859	
330	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	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	312	284	1.09859	
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	312	284	1.09859	
333	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	312	284	1.09859	
334	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	312	284	1.09859	
335	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	312	284	1.09859	
336	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	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	40s ribosomal protein s20. [source:swissprot;acc:p17075]	243.5	267.21	1.09737	
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	241.625	265.136	1.0973	

Legend:
- Rank is the rank after comparing the two networks
- 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/