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 Network Comparison Type Value Type description Filtered Interaction Map network_comparison green red

Results: HTML CSV LaTeX

Showing element 277 to 326 of 3228 in total

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

Rank	description	network_comparison	green	red	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	1.10665	267.642	241.849	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	1.10642	267.088	241.399	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	1.10605	228.42	252.644	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	1.10578	228.356	252.512	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	1.10557	267.335	241.808	
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]	1.10553	228.297	252.39	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	1.10552	267.346	241.828	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	1.10541	203.235	224.657	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	1.10532	203.242	224.647	
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]	1.1052	203.251	224.633	
287	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	1.10517	266.079	240.758	
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	1.10517	266.078	240.758	
289	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	1.10486	246.892	272.781	
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	1.10428	210.064	231.969	
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]	1.10368	228.037	251.679	
292	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	1.10357	266.414	241.411	
293	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	1.10356	265.717	240.782	
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]	1.10356	265.717	240.782	
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]	1.103	202.423	223.273	
296	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	1.10294	266.12	241.282	
297	60s ribosomal protein l7. [source:swissprot;acc:p18124]	1.1029	259.984	235.727	
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]	1.10281	243.588	268.632	
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]	1.10281	243.592	268.635	
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	1.10196	166.351	150.959	
301	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	1.10193	166.372	150.982	
302	60s ribosomal protein l26. [source:swissprot;acc:q02877]	1.10185	267.008	242.326	
303	60s ribosomal protein l35. [source:swissprot;acc:p42766]	1.10179	266.999	242.333	
304	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	1.1017	266.986	242.339	
305	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	1.1017	266.986	242.339	
306	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	1.10126	266.673	242.153	
307	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	1.10126	266.673	242.153	
308	60s ribosomal protein l34. [source:swissprot;acc:p49207]	1.10126	266.673	242.153	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	1.10126	266.673	242.153	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	1.10126	266.673	242.153	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	1.10108	267.151	242.627	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	1.10103	266.663	242.195	
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	1.10069	211.207	232.473	
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	1.10027	268.604	244.126	
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]	1.10027	268.604	244.126	
316	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	1.10022	267.017	242.694	
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]	1.09998	204.044	224.445	
318	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	1.09987	266.18	242.011	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	1.09969	264.729	240.73	
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	1.0995	265.96	241.892	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	1.09949	265.959	241.892	
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	1.09948	78.8995	86.7483	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	1.09947	265.945	241.884	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	1.09941	268.195	243.944	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	1.09941	268.195	243.944	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	1.09932	265.924	241.899	

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/