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 512 to 561 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
128	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Rooted	48.0515	39.0445	1.23069	
129	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Rooted	54.2343	66.7323	1.23044	
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Measured	4358.13	5811.49	1.33348	
129	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Ranked	94	114	1.21277	
129	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Squared	178263	118639	1.50257	
130	44050 protein. [source:refseq;acc:nm_178832]	Squared	148058	99628.4	1.4861	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Measured	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	55.1026	67.5701	1.22626	
130	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Ranked	94	114	1.21277	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Measured	2234.73	2978.57	1.33285	
131	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Rooted	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	148058	99628.4	1.4861	
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	294.053	242.562	1.21228	
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	Squared	36359.2	24466.8	1.48606	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Measured	2236.61	2980.35	1.33253	
132	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Rooted	44.963	55.0576	1.22451	
132	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Ranked	350	290	1.2069	
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Measured	23421.5	17580.4	1.33225	
133	gbp protein isoform a. [source:refseq;acc:nm_017870]	Squared	1182.25	1726.55	1.46039	
133	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Rooted	45.4558	55.5995	1.22316	
133	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Ranked	350	290	1.2069	
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Ranked	350	290	1.2069	
134	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Rooted	44.849	54.7964	1.2218	
134	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Measured	21785.2	16426.1	1.32626	
134	p66 alpha. [source:refseq;acc:nm_017660]	Squared	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	54.935	66.6101	1.21253	
135	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Measured	21785.2	16426.1	1.32626	
135	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Ranked	350	290	1.2069	
135	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Squared	81888.8	56306.5	1.45434	
136	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Rooted	41.8357	50.6469	1.21061	
136	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Ranked	350	290	1.2069	
136	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Measured	3620.77	4763.34	1.31556	
136	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Squared	81888.8	56306.5	1.45434	
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Measured	3620.77	4763.34	1.31556	
137	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Squared	81606.8	56215.8	1.45167	
137	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Rooted	54.9787	66.2416	1.20486	
137	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Ranked	350	290	1.2069	
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Measured	2755.15	2094.3	1.31555	
138	musashi 1. [source:refseq;acc:nm_002442]	Rooted	54.9787	66.2416	1.20486	
138	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Squared	468498	322755	1.45156	
138	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Ranked	194.372	234.204	1.20493	
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Ranked	271.752	225.68	1.20415	
139	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Squared	81592.1	56211.1	1.45153	
139	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Rooted	54.9787	66.2416	1.20486	
139	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Measured	2759.61	2099.49	1.31442	
140	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Squared	81527.6	56190.6	1.45091	
140	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Rooted	55.6161	66.7332	1.19989	
140	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Measured	2760.28	2100.27	1.31425	
140	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Ranked	59	49	1.20408	
141	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Squared	81520.8	56188.5	1.45084	

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/