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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Filtered Rank Gene description Value Type Network Comparison Type Interaction Map red network_comparison green

Results: HTML CSV LaTeX

Showing element 101 to 150 of 3730 in total

Filtered	0
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	red	network_comparison	green	
101	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	14548.5	1.221	11915.2	
102	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	12738.7	1.22052	10437.1	
103	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	7495.26	1.21815	9130.38	
104	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	9545	1.21314	7868	
105	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [source:swissprot;acc:p45954]	17410.5	1.21243	14360	
106	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]	16290.7	1.20987	13464.8	
107	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	11853.5	1.20845	9808.86	
108	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	10585.3	1.2063	12769.1	
109	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	14466.8	1.20239	12031.7	
110	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	12584.5	1.20189	10470.6	
111	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	9940.69	1.20002	11929	
112	40s ribosomal protein s26. [source:swissprot;acc:p02383]	14269.7	1.1982	17098	
113	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	5673.33	1.19816	6797.56	
114	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	8871.11	1.19525	10603.2	
115	spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	18662.8	1.19427	15627	
116	metaxin 1. [source:swissprot;acc:q13505]	13761.3	1.19335	16422.1	
117	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	11545	1.19285	13771.5	
118	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	12049	1.19269	14370.7	
119	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	3609	1.19216	4302.5	
120	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	5797	1.18962	4873	
121	zinc finger protein 232. [source:swissprot;acc:q9uny5]	11523.7	1.18772	13686.9	
122	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	11523	1.18766	13685.4	
123	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	11522.8	1.18764	13684.9	
124	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	11520.7	1.18746	13680.4	
125	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	22038	1.18624	18578	
126	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	9722.71	1.18216	11493.8	
127	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	9411.34	1.18152	11119.7	
128	60s ribosomal protein l39. [source:swissprot;acc:p02404]	11564.4	1.18073	9794.29	
129	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	14222.5	1.17945	12058.6	
130	enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	14476.2	1.17914	17069.5	
131	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	8375.43	1.17887	9873.58	
132	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	19048	1.1754	22389	
133	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	6814	1.17537	8009	
134	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	12314.9	1.17404	10489.3	
135	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	12314.9	1.17404	10489.3	
136	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	12335.3	1.17403	10506.8	
137	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	12328.5	1.17403	10501	
138	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	12384.7	1.17397	10549.4	
139	alpha crystallin a chain. [source:swissprot;acc:p02489]	16372.4	1.17178	13972.2	
140	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	16411.9	1.17001	14027.1	
141	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	7690.02	1.1692	8991.19	
142	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	8214.41	1.16908	7026.41	
143	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_032959]	11124.8	1.16904	13005.3	
144	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_145325]	11123.4	1.16872	13000.1	
145	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	7955.61	1.16694	6817.49	
146	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	12577.8	1.16571	14662.1	
147	60s ribosomal protein l7. [source:swissprot;acc:p18124]	11080.3	1.16562	9505.89	
148	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	6755.71	1.164	7863.63	
149	block 23. [source:sptrembl;acc:q8nhw5]	11469.3	1.16265	13334.8	
150	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	8730	1.16152	7516	

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/