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 582 to 631 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
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	251.679	228.037	1.10368	
292	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	1	241.411	266.414	1.10357	
292	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	0	10280.5	9574.98	1.07368	
293	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	1	240.782	265.717	1.10356	
293	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	0	10287.1	9583.27	1.07344	
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	240.782	265.717	1.10356	
294	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [source:swissprot;acc:q16514]	0	13981.5	13025.1	1.07343	
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	223.273	202.423	1.103	
295	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	0	13687.7	12751.8	1.07339	
296	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [source:swissprot;acc:p36776]	0	10194.1	10941.8	1.07335	
296	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	1	241.282	266.12	1.10294	
297	60s ribosomal protein l7. [source:swissprot;acc:p18124]	1	235.727	259.984	1.1029	
297	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	0	8123.75	8719	1.07327	
298	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	0	11977.8	12842.5	1.07219	
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	268.632	243.588	1.10281	
299	3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	0	12338.7	11512.3	1.07178	
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	268.635	243.592	1.10281	
300	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [source:swissprot;acc:p22612]	0	9270.49	8650.24	1.0717	
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	1	150.959	166.351	1.10196	
301	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	1	150.982	166.372	1.10193	
301	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [source:refseq;acc:nm_015503]	0	12783	13698	1.07158	
302	60s ribosomal protein l26. [source:swissprot;acc:q02877]	1	242.326	267.008	1.10185	
302	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	0	7386.71	6895.44	1.07125	
303	60s ribosomal protein l35. [source:swissprot;acc:p42766]	1	242.333	266.999	1.10179	
303	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	0	11431.4	12244.1	1.07109	
304	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	1	242.339	266.986	1.1017	
304	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	0	8021.78	7496.8	1.07003	
305	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	0	9431	8815	1.06988	
305	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	1	242.339	266.986	1.1017	
306	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	1	242.153	266.673	1.10126	
306	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [source:swissprot;acc:q9np71]	0	5540	5921	1.06877	
307	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	0	1091	1021	1.06856	
307	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	1	242.153	266.673	1.10126	
308	60s ribosomal protein l34. [source:swissprot;acc:p49207]	1	242.153	266.673	1.10126	
308	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	0	11414.1	12191.8	1.06814	
309	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	0	13651	14572	1.06747	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	1	242.153	266.673	1.10126	
310	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	0	9328.78	8741.55	1.06718	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	1	242.153	266.673	1.10126	
311	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	0	10253.5	9622.45	1.06558	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	1	242.627	267.151	1.10108	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	1	242.195	266.663	1.10103	
312	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	0	11959.8	12731.1	1.06449	
313	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	0	11935.6	12698.9	1.06395	
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	1	232.473	211.207	1.10069	
314	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	0	10301.4	10957.5	1.06369	
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	1	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]	1	244.126	268.604	1.10027	
315	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	0	12121.6	12887.6	1.06319	
316	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	0	10768.5	11444	1.06273	

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/