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 Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 277 to 326 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	267.642	241.849	1.10665	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	267.088	241.399	1.10642	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	228.42	252.644	1.10605	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	228.356	252.512	1.10578	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	267.335	241.808	1.10557	
282	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	228.297	252.39	1.10553	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	267.346	241.828	1.10552	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	203.235	224.657	1.10541	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	203.242	224.647	1.10532	
286	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	203.251	224.633	1.1052	
287	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	266.079	240.758	1.10517	
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	266.078	240.758	1.10517	
289	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	246.892	272.781	1.10486	
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	210.064	231.969	1.10428	
291	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	228.037	251.679	1.10368	
292	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	266.414	241.411	1.10357	
293	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	265.717	240.782	1.10356	
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]	265.717	240.782	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]	202.423	223.273	1.103	
296	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	266.12	241.282	1.10294	
297	60s ribosomal protein l7. [source:swissprot;acc:p18124]	259.984	235.727	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]	243.588	268.632	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]	243.592	268.635	1.10281	
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	166.351	150.959	1.10196	
301	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	166.372	150.982	1.10193	
302	60s ribosomal protein l26. [source:swissprot;acc:q02877]	267.008	242.326	1.10185	
303	60s ribosomal protein l35. [source:swissprot;acc:p42766]	266.999	242.333	1.10179	
304	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	266.986	242.339	1.1017	
305	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	266.986	242.339	1.1017	
306	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	266.673	242.153	1.10126	
307	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	266.673	242.153	1.10126	
308	60s ribosomal protein l34. [source:swissprot;acc:p49207]	266.673	242.153	1.10126	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	266.673	242.153	1.10126	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	266.673	242.153	1.10126	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	267.151	242.627	1.10108	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	266.663	242.195	1.10103	
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	211.207	232.473	1.10069	
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	268.604	244.126	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]	268.604	244.126	1.10027	
316	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	267.017	242.694	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]	204.044	224.445	1.09998	
318	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	266.18	242.011	1.09987	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	264.729	240.73	1.09969	
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	265.96	241.892	1.0995	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	265.959	241.892	1.09949	
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	78.8995	86.7483	1.09948	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	265.945	241.884	1.09947	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	268.195	243.944	1.09941	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	268.195	243.944	1.09941	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	265.924	241.899	1.09932	

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/