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 518 to 567 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Divided	227.999	204.37	1.11562	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Divided	219.421	196.978	1.11394	
260	surfeit locus protein 5. [source:swissprot;acc:q15528]	Subtracted	242.14	265.696	23.556	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Divided	219.421	196.978	1.11394	
261	zinc finger protein 291. [source:swissprot;acc:q9by12]	Subtracted	242.14	265.696	23.556	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Divided	219.421	196.978	1.11394	
262	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Subtracted	242.14	265.696	23.556	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Divided	219.421	196.978	1.11394	
263	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Subtracted	242.14	265.696	23.556	
264	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Subtracted	243.24	266.796	23.556	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Divided	219.421	196.978	1.11394	
265	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Subtracted	240.243	263.798	23.555	
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]	Divided	225.217	202.459	1.11241	
266	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Subtracted	243.12	266.662	23.542	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Divided	241.07	267.88	1.11121	
267	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Subtracted	243.12	266.661	23.541	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Divided	241.07	267.88	1.11121	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Divided	271.016	244.167	1.10996	
268	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Subtracted	241.625	265.136	23.511	
269	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Subtracted	241.625	265.136	23.511	
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]	Divided	241.373	267.352	1.10763	
270	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Subtracted	241.612	265.119	23.507	
270	fad synthetase. [source:refseq;acc:nm_025207]	Divided	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]	Divided	241.373	267.352	1.10763	
271	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	Subtracted	243.072	266.559	23.487	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Divided	241.373	267.352	1.10763	
272	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	Subtracted	242.83	266.248	23.418	
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]	Divided	241.373	267.352	1.10763	
273	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Subtracted	243.208	266.617	23.409	
274	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Subtracted	242.744	266.07	23.326	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Divided	241.373	267.352	1.10763	
275	40s ribosomal protein s5. [source:swissprot;acc:p46782]	Subtracted	242.473	265.756	23.283	
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]	Divided	241.373	267.352	1.10763	
276	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Divided	241.13	266.969	1.10716	
276	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Subtracted	258.437	235.183	23.254	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Divided	241.849	267.642	1.10665	
277	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	Subtracted	239.277	262.434	23.157	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Divided	241.399	267.088	1.10642	
278	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Subtracted	235.383	258.476	23.093	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Divided	252.644	228.42	1.10605	
279	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	Subtracted	242.66	265.715	23.055	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Divided	252.512	228.356	1.10578	
280	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Subtracted	267.208	244.168	23.04	
281	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Subtracted	242.159	265.104	22.945	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Divided	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]	Divided	252.39	228.297	1.10553	
282	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Subtracted	242.159	265.104	22.945	
283	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Subtracted	242.37	265.255	22.885	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Divided	241.828	267.346	1.10552	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Divided	224.657	203.235	1.10541	

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/