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 262 to 311 of 3228 in total

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

Rank	description	red	green	network_comparison	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	219.421	196.978	1.11394	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	219.421	196.978	1.11394	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	219.421	196.978	1.11394	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	225.217	202.459	1.11241	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	241.07	267.88	1.11121	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	241.07	267.88	1.11121	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	271.016	244.167	1.10996	
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	241.373	267.352	1.10763	
270	fad synthetase. [source:refseq;acc:nm_025207]	241.373	267.352	1.10763	
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	241.373	267.352	1.10763	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	241.373	267.352	1.10763	
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	241.373	267.352	1.10763	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	241.373	267.352	1.10763	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	241.373	267.352	1.10763	
276	60s ribosomal protein l32. [source:swissprot;acc:p02433]	241.13	266.969	1.10716	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	241.849	267.642	1.10665	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	241.399	267.088	1.10642	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	252.644	228.42	1.10605	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	252.512	228.356	1.10578	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	241.808	267.335	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]	252.39	228.297	1.10553	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	241.828	267.346	1.10552	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	224.657	203.235	1.10541	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	224.647	203.242	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]	224.633	203.251	1.1052	
287	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	240.758	266.079	1.10517	
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	240.758	266.078	1.10517	
289	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	272.781	246.892	1.10486	
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	231.969	210.064	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]	251.679	228.037	1.10368	
292	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	241.411	266.414	1.10357	
293	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	240.782	265.717	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]	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	

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/