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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1030 to 1079 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
129	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Rooted	0	27.8028	22.9122	1.21345	
129	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Squared	1	178263	118639	1.50257	
129	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Measured	0	606.485	454.837	1.33341	
130	44050 protein. [source:refseq;acc:nm_178832]	Squared	1	148058	99628.4	1.4861	
130	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Squared	0	21165.1	38499.2	1.81899	
130	enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	Ranked	0	14476.2	17069.5	1.17914	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Measured	1	2234.68	2978.53	1.33287	
130	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Rooted	1	55.1026	67.5701	1.22626	
130	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Measured	0	42	56	1.33333	
130	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Ranked	1	94	114	1.21277	
130	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Rooted	0	12.7347	10.4997	1.21286	
131	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	Rooted	0	19.3128	16.0484	1.20341	
131	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Ranked	0	8375.43	9873.58	1.17887	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Measured	1	2234.73	2978.57	1.33285	
131	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Rooted	1	55.1113	67.5537	1.22577	
131	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	Squared	1	148058	99628.4	1.4861	
131	serpin b11. [source:swissprot;acc:q96p15]	Measured	0	42	56	1.33333	
131	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Ranked	1	294.053	242.562	1.21228	
131	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Squared	0	451.156	817.981	1.81308	
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	Squared	1	36359.2	24466.8	1.48606	
132	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	Rooted	0	23.9003	19.8655	1.20311	
132	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Measured	0	42	56	1.33333	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Measured	1	2236.61	2980.35	1.33253	
132	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Rooted	1	44.963	55.0576	1.22451	
132	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Squared	0	1.75053	0.969467	1.80566	
132	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Ranked	0	19048	22389	1.1754	
132	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Ranked	1	350	290	1.2069	
133	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	Ranked	0	6814	8009	1.17537	
133	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Measured	0	252	335	1.32937	
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Measured	1	23421.5	17580.4	1.33225	
133	gbp protein isoform a. [source:refseq;acc:nm_017870]	Squared	1	1182.25	1726.55	1.46039	
133	metaxin 1. [source:swissprot;acc:q13505]	Squared	0	6149.89	3429.64	1.79316	
133	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Rooted	1	45.4558	55.5995	1.22316	
133	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	Rooted	0	27.4578	22.8323	1.20259	
133	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Ranked	1	350	290	1.2069	
134	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]	Squared	0	11625.2	6483.52	1.79304	
134	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Ranked	0	12314.9	10489.3	1.17404	
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Ranked	1	350	290	1.2069	
134	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Rooted	0	10	12	1.2	
134	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Rooted	1	44.849	54.7964	1.2218	
134	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Measured	1	21785.2	16426.1	1.32626	
134	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	Measured	0	260.986	346.751	1.32862	
134	p66 alpha. [source:refseq;acc:nm_017660]	Squared	1	81888.8	56306.5	1.45434	
135	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Rooted	1	54.935	66.6101	1.21253	
135	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Measured	1	21785.2	16426.1	1.32626	
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]	Ranked	0	12314.9	10489.3	1.17404	
135	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Ranked	1	350	290	1.2069	
135	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	Measured	0	814.485	613.614	1.32736	
135	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Squared	0	21101.4	11769.5	1.79289	
135	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [source:swissprot;acc:q13813]	Rooted	0	42.8135	51.3517	1.19943	

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/