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 1130 to 1179 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
565	sedlin. [source:swissprot;acc:o14582]	Divided	129.219	121.261	1.06563	
566	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Subtracted	220.744	207.121	13.623	
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Divided	129.219	121.261	1.06563	
567	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	Subtracted	228.639	242.258	13.619	
567	bet3 homolog. [source:swissprot;acc:o43617]	Divided	129.219	121.261	1.06563	
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Divided	226.3	212.38	1.06554	
568	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	Subtracted	228.639	242.258	13.619	
569	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	Subtracted	228.639	242.258	13.619	
569	t54 protein. [source:swissprot;acc:q92917]	Divided	226.3	212.38	1.06554	
570	sorting nexin 17. [source:swissprot;acc:q15036]	Subtracted	228.639	242.258	13.619	
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Divided	229.709	215.631	1.06529	
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	Divided	238.529	254.099	1.06528	
571	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	Subtracted	221.807	208.264	13.543	
572	cbf1 interacting corepressor. [source:refseq;acc:nm_004882]	Divided	227.86	213.945	1.06504	
572	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	Subtracted	221.807	208.264	13.543	
573	autoantigen ngp-1. [source:swissprot;acc:q13823]	Subtracted	250.302	236.817	13.485	
573	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	Divided	227.86	213.945	1.06504	
574	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	Subtracted	237.554	250.823	13.269	
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	Divided	221.807	208.264	1.06503	
575	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	Divided	221.807	208.264	1.06503	
575	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	Subtracted	223.282	210.136	13.146	
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	Divided	235.18	250.419	1.0648	
576	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	Subtracted	232.469	245.613	13.144	
577	60s ribosomal protein l15. [source:swissprot;acc:p39030]	Subtracted	217.862	230.978	13.116	
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Divided	224.606	210.944	1.06477	
578	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]	Subtracted	15	28	13	
578	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	Divided	224.606	210.944	1.06477	
579	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	15	28	13	
579	zinc finger protein t86. [source:swissprot;acc:o00488]	Divided	246.805	231.796	1.06475	
580	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	15	28	13	
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [source:refseq;acc:nm_014596]	Divided	236.751	252.038	1.06457	
581	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	15	28	13	
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [source:swissprot;acc:o43711]	Divided	237.28	252.492	1.06411	
582	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	15	28	13	
582	homeobox protein barh-like 1. [source:swissprot;acc:q9hbu1]	Divided	237.28	252.492	1.06411	
583	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Subtracted	233.725	220.751	12.974	
583	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	Divided	237.28	252.492	1.06411	
584	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Subtracted	233.725	220.751	12.974	
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	Divided	237.28	252.492	1.06411	
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	Divided	237.28	252.492	1.06411	
585	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Subtracted	207.222	194.262	12.96	
586	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	Divided	237.28	252.492	1.06411	
586	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Subtracted	217.215	204.279	12.936	
587	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	Divided	237.28	252.492	1.06411	
587	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]	Subtracted	217.67	230.596	12.926	
588	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	Subtracted	217.67	230.596	12.926	
588	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	Divided	216.557	230.362	1.06375	
589	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	Subtracted	217.67	230.596	12.926	
589	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Divided	228.215	214.546	1.06371	
590	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	Subtracted	217.67	230.596	12.926	

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/