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 1030 to 1079 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
129	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Rooted	0	27.8028	22.9122	1.21345
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	1	178263	118639	1.50257
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured	0	606.485	454.837	1.33341
130	44050 protein. [refseq;acc:nm_178832]	Squared	1	148058	99628.4	1.4861
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Squared	0	21165.1	38499.2	1.81899
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Ranked	0	14476.2	17069.5	1.17914
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Measured	1	2234.68	2978.53	1.33287
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted	1	55.1026	67.5701	1.22626
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Measured	0	42	56	1.33333
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	1	94	114	1.21277
	ubiquitin activating enzyme e1-like protein. [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). [swissprot;acc:p35268]	Rooted		19.3128	16.0484	1.20341
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Ranked		8375.43	9873.58	1.17887
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	1	2234.73	2978.57	1.33285
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted		55.1113	67.5537	1.22577
	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)]. [swissprot;acc:q12972]	Squared		148058	99628.4	1.4861
	serpin b11. [swissprot;acc:q96p15]	Measured	0	42	56	1.33333
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Ranked	1	294.053	242.562	1.21228
	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). [swissprot;acc:o95670]	Squared	0	451.156	817.981	1.81308
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared	1	36359.2	24466.8	1.48606
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Rooted	0	23.9003	19.8655	1.20311
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Measured	0	42	56	1.33333
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Measured	1	2236.61	2980.35	1.33253
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Rooted	1	44.963	55.0576	1.22451
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Squared	0	1.75053	0.969467	1.80566
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Ranked	0	19048	22389	1.1754
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		1	350	290	1.2069
133	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		0	6814	8009	1.17537
	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)]. [swissprot;acc:o95340]	Measured	0	252	335	1.32937
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	1	23421.5	17580.4	1.33225
	gbp protein isoform a. [refseq;acc:nm_017870]	Squared	1	1182.25	1726.55	1.46039
	metaxin 1. [swissprot;acc:q13505]	Squared	0	6149.89	3429.64	1.79316
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Rooted	1	45.4558	55.5995	1.22316
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Rooted	0	27.4578	22.8323	1.20259
	tob1 protein (transducer of erbb-2 1). [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). [swissprot;acc:p41181]	Squared	0	11625.2	6483.52	1.79304
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Ranked	0	12314.9	10489.3	1.17404
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Ranked	1	350	290	1.2069
	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Rooted	0	10	12	1.2
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Rooted	1	44.849	54.7964	1.2218
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Measured	1	21785.2	16426.1	1.32626
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Measured	0	260.986	346.751	1.32862
	p66 alpha. [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). [swissprot;acc:p52298]	Rooted		54.935	66.6101	1.21253
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Measured		21785.2	16426.1	1.32626
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Ranked	0	12314.9	10489.3	1.17404
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked	1	350	290	1.2069
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Measured	0	814.485	613.614	1.32736
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Squared		21101.4	11769.5	1.79289
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Rooted		42.8135	51.3517	1.19943

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/