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 3030 to 3079 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
758	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Squared	20248.9	23608.3	1.16591	
758	phospholipid transfer protein precursor (lipid transfer protein ii). [source:swissprot;acc:p55058]	Ranked	224.434	235.583	1.04968	
758	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Rooted	96.6463	103.103	1.06681	
759	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	Measured	4254.62	4736.03	1.11315	
759	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Squared	49280.5	42272.7	1.16578	
759	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Rooted	66.9416	71.4055	1.06668	
759	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	Ranked	231.809	243.289	1.04952	
760	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Measured	5870.2	6533.39	1.11298	
760	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	Squared	21186.4	24698.3	1.16576	
760	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Rooted	66.9397	71.4023	1.06667	
760	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Ranked	246.055	234.458	1.04946	
761	alpha-nac protein. [source:sptrembl;acc:q9h009]	Rooted	66.9404	71.4035	1.06667	
761	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	Ranked	213.325	203.303	1.0493	
761	translation initiation factor if-2. [source:swissprot;acc:o60841]	Measured	5811.51	6467.62	1.1129	
761	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	Squared	21186.4	24698.3	1.16576	
762	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	Ranked	213.256	203.237	1.0493	
762	di-ras2. [source:refseq;acc:nm_017594]	Rooted	66.9397	71.4022	1.06666	
762	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Measured	6231.31	6933.9	1.11275	
762	pp1201 protein. [source:refseq;acc:nm_022152]	Squared	21186.4	24698.3	1.16576	
763	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	Measured	4250.54	4729.67	1.11272	
763	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	Squared	21186.4	24698.3	1.16576	
763	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Ranked	228.78	218.091	1.04901	
763	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Rooted	60.3269	64.3387	1.0665	
764	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	Measured	4250.18	4729.12	1.11269	
764	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Rooted	63.5181	67.7402	1.06647	
764	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	Squared	21186.4	24698.3	1.16576	
764	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	Ranked	222.082	211.707	1.04901	
765	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	Ranked	229.045	218.343	1.04901	
765	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [source:refseq;acc:nm_006999]	Measured	4726.38	5258.95	1.11268	
765	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	Squared	21186.4	24698.3	1.16576	
765	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Rooted	63.5181	67.7402	1.06647	
766	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	Squared	24509.4	28571.6	1.16574	
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [source:swissprot;acc:q9h2d6]	Ranked	213.804	224.226	1.04875	
766	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Rooted	63.5181	67.7402	1.06647	
766	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	Measured	6691.93	7445.09	1.11255	
767	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Rooted	63.5181	67.7402	1.06647	
767	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	Squared	24509.4	28571.6	1.16574	
767	rho interacting protein 3. [source:refseq;acc:nm_015134]	Ranked	213.803	224.224	1.04874	
767	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [source:swissprot;acc:q16851]	Measured	6691.21	7444.22	1.11254	
768	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [source:swissprot;acc:q9udy4]	Ranked	210.946	221.225	1.04873	
768	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Squared	12108.4	14114.6	1.16569	
768	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	Rooted	63.5181	67.7402	1.06647	
768	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [source:refseq;acc:nm_003350]	Measured	6690.44	7443.29	1.11253	
769	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Rooted	55.6817	59.3786	1.06639	
769	cab2. [source:refseq;acc:nm_033419]	Ranked	210.946	221.225	1.04873	
769	n-acetylglutamate synthase. [source:refseq;acc:nm_153006]	Squared	20943	24412.8	1.16568	
769	vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [source:swissprot;acc:q16864]	Measured	5873.77	6532.44	1.11214	
770	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Rooted	55.6817	59.3786	1.06639	
770	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [source:swissprot;acc:o75953]	Ranked	210.946	221.225	1.04873	
770	fibulin-2 precursor. [source:swissprot;acc:p98095]	Squared	45189.6	52666.2	1.16545	

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/