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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

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Showing element 2501 to 2550 of 16578 in total

Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
626	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	Divided	High confidence	214.256	202.14	1.05994	
626	HEYL	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	Subtracted	High confidence	229.072	216.576	12.496	
626	HIST3H3	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Divided	Low confidence	204.239	198.436	1.02924	
626	HIST3H3	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Subtracted	Low confidence	204.239	198.436	5.803	
627		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Subtracted	Low confidence	204.234	198.433	5.801	
627	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	Divided	High confidence	214.256	202.139	1.05994	
627	P4HB	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	Divided	Low confidence	204.369	198.564	1.02923	
627	SYN2	synapsin ii. [source:swissprot;acc:q92777]	Subtracted	High confidence	229.072	216.576	12.496	
628		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Divided	Low confidence	204.234	198.433	1.02923	
628	CUL1	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Subtracted	Low confidence	203.853	198.057	5.796	
628	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	Divided	High confidence	214.256	202.14	1.05994	
628	MRRF	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	Subtracted	High confidence	229.072	216.576	12.496	
629		histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Subtracted	Low confidence	204.242	198.448	5.794	
629	GABRA3	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Divided	High confidence	214.256	202.14	1.05994	
629	P4HA1	prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [source:swissprot;acc:p13674]	Divided	Low confidence	204.369	198.564	1.02923	
629	PEX5	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	Subtracted	High confidence	229.072	216.576	12.496	
630		dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Subtracted	Low confidence	204.242	198.448	5.794	
630	HEY2	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	Subtracted	High confidence	229.072	216.576	12.496	
630	NDUFA6	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	Divided	High confidence	214.256	202.141	1.05993	
630	P4HA2	prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [source:swissprot;acc:o15460]	Divided	Low confidence	204.369	198.564	1.02923	
631		histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Divided	Low confidence	204.242	198.448	1.0292	
631	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Subtracted	High confidence	229.072	216.576	12.496	
631	MARCH6	similar to s. cerevisiae ssm4. [source:refseq;acc:nm_005885]	Subtracted	Low confidence	207.662	201.876	5.786	
631	PDXDC1	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	Divided	High confidence	214.256	202.141	1.05993	
632		dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Divided	Low confidence	204.242	198.448	1.0292	
632		large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [source:swissprot;acc:p46379]	Subtracted	Low confidence	207.662	201.876	5.786	
632	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Subtracted	High confidence	229.072	216.576	12.496	
632	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Divided	High confidence	214.254	202.166	1.05979	
633		dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [source:swissprot;acc:q92685]	Subtracted	Low confidence	200.085	194.301	5.784	
633	AARS	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	Divided	High confidence	234.106	248.104	1.05979	
633	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Subtracted	High confidence	229.072	216.576	12.496	
633	TMBIM1	pp1201 protein. [source:refseq;acc:nm_022152]	Divided	Low confidence	203.734	197.956	1.02919	
634		dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Divided	High confidence	226.523	213.786	1.05958	
634	SYN1	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Subtracted	High confidence	229.072	216.576	12.496	
634	TMBIM1	pp1201 protein. [source:refseq;acc:nm_022152]	Subtracted	Low confidence	203.734	197.956	5.778	
634	TSC22D4	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [source:swissprot;acc:q9y3q8]	Divided	Low confidence	203.726	197.955	1.02915	
635	BBS7	bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [source:refseq;acc:nm_176824]	Divided	Low confidence	207.763	201.882	1.02913	
635	MVK	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	Subtracted	High confidence	235.296	247.673	12.377	
635	RPL37	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	Divided	High confidence	228.639	242.258	1.05957	
635	TSC22D4	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [source:swissprot;acc:q9y3q8]	Subtracted	Low confidence	203.726	197.955	5.771	
636	N6AMT1	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Subtracted	Low confidence	204.933	199.164	5.769	
636	RBM19	probable rna-binding protein kiaa0682. [source:swissprot;acc:q9y4c8]	Divided	Low confidence	206.001	200.193	1.02901	
636	SFRS1	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	Divided	High confidence	228.639	242.258	1.05957	
636	VAV1	vav proto-oncogene. [source:swissprot;acc:p15498]	Subtracted	High confidence	212.2	199.849	12.351	
637	AGPAT3	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]	Divided	Low confidence	192.166	186.751	1.029	
637	PPAT	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	Divided	High confidence	228.639	242.258	1.05957	
637	RNF144B	ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [source:sptrembl;acc:q9bx39]	Subtracted	Low confidence	208.62	202.855	5.765	
637	VAV3	vav-3 protein. [source:swissprot;acc:q9ukw4]	Subtracted	High confidence	212.253	199.908	12.345	
638	NUFIP1	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [source:refseq;acc:nm_012345]	Divided	Low confidence	203.825	198.081	1.029	
638	SNX17	sorting nexin 17. [source:swissprot;acc:q15036]	Divided	High confidence	228.639	242.258	1.05957	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/