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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 627 to 676 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
314	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Subtracted	6563.65	7627.29	1063.64	
314	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Divided	21632.5	18090	1.19583	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Divided	21370.8	17896.5	1.19413	
315	vav proto-oncogene. [source:swissprot;acc:p15498]	Subtracted	6644.99	7707.8	1062.81	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Divided	21370.8	17896.5	1.19413	
316	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Subtracted	6603.41	7664.65	1061.24	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Divided	3153.1	3762.56	1.19329	
317	vav-3 protein. [source:swissprot;acc:q9ukw4]	Subtracted	6647.43	7706.18	1058.75	
318	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Subtracted	7485.08	8543.66	1058.58	
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Divided	34190.9	40795.8	1.19318	
319	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Subtracted	7477	8532.02	1055.02	
319	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Divided	20911	24908.5	1.19117	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Divided	20911	24908.5	1.19117	
320	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	Subtracted	10263.8	11318.6	1054.8	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Divided	20911	24908.5	1.19117	
321	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Subtracted	11797.1	10750.2	1046.9	
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Divided	20911	24908.5	1.19117	
322	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Subtracted	9304.83	10347.3	1042.47	
323	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	Subtracted	10247.8	11289	1041.2	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Divided	4620.76	5501.94	1.1907	
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Divided	28136.5	33457.6	1.18912	
324	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	Subtracted	11773.7	10733.8	1039.9	
325	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	Subtracted	8362.81	9402.7	1039.89	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Divided	16177.9	19235.4	1.18899	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Divided	3432.96	4081.21	1.18883	
326	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	Subtracted	11773	10733.2	1039.8	
327	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	Subtracted	11773	10733.2	1039.8	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Divided	16067.4	19094.4	1.18839	
328	brain protein 44. [source:swissprot;acc:o95563]	Divided	15999.1	19007.1	1.18801	
328	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Subtracted	11773	10733.2	1039.8	
329	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	Subtracted	11773	10733.2	1039.8	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Divided	15999.1	19007.1	1.18801	
330	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	Subtracted	11773	10733.2	1039.8	
330	septin 6. [source:swissprot;acc:q14141]	Divided	15959.9	18957.1	1.1878	
331	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Subtracted	10246.1	11285.8	1039.7	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Divided	20287.2	17083.8	1.18751	
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Divided	5051.16	5975.51	1.183	
332	vav-2 protein. [source:swissprot;acc:p52735]	Subtracted	6660.02	7697.78	1037.76	
333	deltex 2. [source:refseq;acc:nm_020892]	Subtracted	1618.84	2651.88	1033.04	
333	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Divided	5039.63	5961.83	1.18299	
334	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Subtracted	1629.21	2662.12	1032.91	
334	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Divided	14924.4	17655.2	1.18298	
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Divided	3494.31	4129.6	1.18181	
335	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Subtracted	1631.67	2664.55	1032.88	
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Divided	3751.3	4431.34	1.18128	
336	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Subtracted	1631.67	2664.55	1032.88	
337	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	20446.1	24136.4	1.18049	
337	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Subtracted	1631.67	2664.55	1032.88	
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Divided	20446.1	24136.4	1.18049	
338	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Subtracted	1631.67	2664.55	1032.88	

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/