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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1058 to 1107 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
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	
135	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Squared	1	81888.8	56306.5	1.45434	
136	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Rooted	1	41.8357	50.6469	1.21061	
136	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	Ranked	0	12335.3	10506.8	1.17403	
136	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Ranked	1	350	290	1.2069	
136	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Rooted	0	23.9877	20.1222	1.1921	
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	1	3620.77	4763.34	1.31556	
136	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Squared	0	978.105	1746.18	1.78527	
136	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Measured	0	1526.38	1150.51	1.3267	
136	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Squared	1	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	1	3620.77	4763.34	1.31556	
137	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Squared	1	81606.8	56215.8	1.45167	
137	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	Ranked	0	12328.5	10501	1.17403	
137	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	Measured	0	1631.18	1233.41	1.3225	
137	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Squared	0	0.417515	0.742249	1.77778	
137	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Rooted	1	54.9787	66.2416	1.20486	
137	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Ranked	1	350	290	1.2069	
137	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Rooted	0	18.9056	15.8624	1.19185	
138	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	Rooted	0	22.775	19.1245	1.19088	
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Measured	1	2755.15	2094.3	1.31555	
138	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	Ranked	0	12384.7	10549.4	1.17397	
138	musashi 1. [source:refseq;acc:nm_002442]	Rooted	1	54.9787	66.2416	1.20486	
138	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Squared	1	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	1	194.372	234.204	1.20493	
138	serpin b11. [source:swissprot;acc:q96p15]	Squared	0	0.417515	0.742249	1.77778	
138	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	Measured	0	204.382	154.804	1.32026	
139	alpha crystallin a chain. [source:swissprot;acc:p02489]	Ranked	0	16372.4	13972.2	1.17178	
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	1	271.752	225.68	1.20415	
139	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Measured	0	736.737	561.038	1.31317	

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/