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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Gene Rank description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1875 to 1924 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
938	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Subtracted	212.442	205.087	7.355	
938	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	Divided	220.246	212.618	1.03588	
939	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	Divided	216.501	224.27	1.03588	
939	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	Subtracted	212.44	205.085	7.355	
940	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	Divided	212.442	205.088	1.03586	
940	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	Subtracted	212.442	205.088	7.354	
941	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	Divided	212.437	205.083	1.03586	
941	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	Subtracted	212.437	205.083	7.354	
942	grancalcin. [source:swissprot;acc:p28676]	Divided	212.442	205.088	1.03586	
942	grancalcin. [source:swissprot;acc:p28676]	Subtracted	212.442	205.088	7.354	
943	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	Subtracted	212.437	205.083	7.354	
943	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Divided	212.442	205.087	1.03586	
944	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Subtracted	212.51	205.191	7.319	
944	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	Divided	212.437	205.083	1.03586	
945	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	Divided	212.44	205.085	1.03586	
945	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Subtracted	229.116	221.823	7.293	
946	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Subtracted	225.557	218.271	7.286	
946	histone h4. [source:swissprot;acc:p02304]	Divided	227.765	219.902	1.03576	
947	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Divided	212.51	205.191	1.03567	
947	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Subtracted	177.776	170.499	7.277	
948	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Subtracted	225.167	217.922	7.245	
948	target of myb protein 1. [source:swissprot;acc:o60784]	Divided	217.254	209.824	1.03541	
949	huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	Divided	217.253	209.826	1.0354	
949	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Subtracted	225.167	217.922	7.245	
950	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [source:swissprot;acc:p28715]	Divided	252.873	261.821	1.03539	
950	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Subtracted	225.167	217.922	7.245	
951	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Subtracted	225.167	217.922	7.245	
951	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	Divided	217.253	209.827	1.03539	
952	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Subtracted	225.448	218.232	7.216	
952	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	Divided	217.252	209.83	1.03537	
953	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Subtracted	178.033	170.82	7.213	
953	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [source:swissprot;acc:q01780]	Divided	198.494	205.466	1.03512	
954	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	Divided	267.447	276.773	1.03487	
954	thioredoxin-like; pkc-interacting cousin of thioredoxin. [source:refseq;acc:nm_006541]	Subtracted	228.412	235.609	7.197	
955	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	Subtracted	221.73	228.906	7.176	
955	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	Divided	231.163	239.205	1.03479	
956	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Subtracted	135.379	128.225	7.154	
956	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	Divided	211.812	204.732	1.03458	
957	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Divided	129.913	134.399	1.03453	
957	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	Subtracted	168.592	161.452	7.14	
958	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Divided	129.921	134.406	1.03452	
958	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Subtracted	218.459	211.338	7.121	
959	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]	Divided	237.558	229.677	1.03431	
959	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Subtracted	218.461	211.343	7.118	
960	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Subtracted	218.462	211.345	7.117	
960	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Divided	237.558	229.677	1.03431	
961	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Subtracted	218.468	211.357	7.111	
961	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Divided	130.066	134.527	1.0343	
962	cyclin g2. [source:swissprot;acc:q16589]	Divided	130.066	134.527	1.0343	
962	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	Subtracted	219.656	212.547	7.109	

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/