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 1075 to 1124 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
538	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Subtracted	6228.39	7013.19	784.8	
538	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Divided	10603.5	12069.4	1.13825	
539	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	Subtracted	6228.39	7013.19	784.8	
539	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	Divided	10603.5	12069.4	1.13825	
540	gk001 protein. [source:refseq;acc:nm_020198]	Divided	10603.5	12069.4	1.13825	
540	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Subtracted	6228.39	7013.19	784.8	
541	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	Divided	10600.3	12065.2	1.13819	
541	limkain b1. [source:refseq;acc:nm_019081]	Subtracted	6228.39	7013.19	784.8	
542	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	Subtracted	6228.39	7013.19	784.8	
542	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	Divided	3889.27	4426.74	1.13819	
543	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	Divided	10599.9	12064.7	1.13819	
543	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Subtracted	6228.39	7013.19	784.8	
544	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	Subtracted	6228.39	7013.19	784.8	
544	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [source:swissprot;acc:q9y243]	Divided	3889.27	4426.74	1.13819	
545	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	Subtracted	6228.39	7013.19	784.8	
545	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	Divided	3889.27	4426.74	1.13819	
546	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Subtracted	6228.39	7013.19	784.8	
546	zinc finger protein t86. [source:swissprot;acc:o00488]	Divided	4052.77	4612.54	1.13812	
547	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Subtracted	6228.39	7013.19	784.8	
547	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Divided	5291.92	6020.19	1.13762	
548	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Divided	8268.19	9405.85	1.13759	
548	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Subtracted	6228.39	7013.19	784.8	
549	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Divided	5865.79	6671.23	1.13731	
549	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	Subtracted	6228.42	7013.21	784.79	
550	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Subtracted	6228.97	7013.53	784.56	
550	prohibitin. [source:swissprot;acc:p35232]	Divided	5773.45	6563.69	1.13687	
551	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	Subtracted	6503.1	7282.94	779.84	
551	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Divided	5773.45	6563.69	1.13687	
552	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	Subtracted	6503.03	7282.5	779.47	
552	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	Divided	15427.2	13572.8	1.13663	
553	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	Subtracted	10430.3	9656.4	773.9	
553	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Divided	3853.64	4379.71	1.13651	
554	dendritic cell protein. [source:refseq;acc:nm_006360]	Subtracted	6593.17	7364.55	771.38	
554	pre-mrna cleavage complex ii protein clp1. [source:swissprot;acc:q92989]	Divided	14830.5	13050.3	1.13641	
555	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	Subtracted	6593.17	7364.55	771.38	
555	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Divided	6167.93	7007.7	1.13615	
556	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	Subtracted	6593.17	7364.55	771.38	
556	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Divided	6167.93	7007.7	1.13615	
557	cpz gene product. [source:refseq;acc:nm_003652]	Subtracted	6593.17	7364.55	771.38	
557	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Divided	6167.93	7007.7	1.13615	
558	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	Subtracted	6593.17	7364.55	771.38	
558	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Divided	6167.93	7007.7	1.13615	
559	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Divided	6167.93	7007.7	1.13615	
559	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	Subtracted	6593.17	7364.55	771.38	
560	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Divided	5480.24	6222.04	1.13536	
560	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Subtracted	6374.65	7145.59	770.94	
561	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Divided	5480.24	6222.04	1.13536	
561	tubby protein homolog. [source:swissprot;acc:p50607]	Subtracted	6374.65	7145.59	770.94	
562	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Subtracted	6374.65	7145.59	770.94	
562	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Divided	5480.24	6222.04	1.13536	

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/