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 2930 to 2979 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
733	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Measured	13241.4	11864	1.1161	
733	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	Rooted	52.0099	55.5904	1.06884	
733	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [source:swissprot;acc:q13488]	Squared	26029.1	30413.6	1.16845	
734	loh1cr12. [source:refseq;acc:nm_058169]	Rooted	57.805	61.7803	1.06877	
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	Ranked	232.601	244.534	1.0513	
734	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Measured	13241.4	11864	1.1161	
734	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [source:swissprot;acc:q93050]	Squared	26032.5	30417.7	1.16845	
735	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [source:refseq;acc:nm_020632]	Squared	26030.5	30415.2	1.16844	
735	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	Ranked	232.601	244.534	1.0513	
735	unr protein. [source:swissprot;acc:o75534]	Rooted	57.805	61.7803	1.06877	
735	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [source:swissprot;acc:p27449]	Measured	5768.32	6434.78	1.11554	
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Ranked	232.601	244.534	1.0513	
736	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	Squared	22017.1	25721.9	1.16827	
736	sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	Measured	5768.32	6434.78	1.11554	
736	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	Rooted	51.5438	55.0853	1.06871	
737	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [source:refseq;acc:nm_022735]	Measured	5768.32	6434.78	1.11554	
737	pnas-18. [source:sptrembl;acc:q9bzu3]	Rooted	97.8205	91.5467	1.06853	
737	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Ranked	125.526	119.402	1.05129	
737	transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	Squared	31479.4	36770.8	1.16809	
738	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	Measured	5768.32	6434.78	1.11554	
738	syntaxin 7. [source:swissprot;acc:o15400]	Rooted	61.5022	65.7076	1.06838	
738	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	Squared	31467.1	36752.2	1.16796	
738	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	Ranked	222.825	211.966	1.05123	
739	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	Measured	5768.32	6434.78	1.11554	
739	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	Rooted	65.3677	69.828	1.06823	
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	Ranked	223.58	235.027	1.0512	
739	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [source:swissprot;acc:o75792]	Squared	25727.7	30046.7	1.16787	
740	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [source:swissprot;acc:p31939]	Ranked	223.58	235.027	1.0512	
740	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	Rooted	53.1114	56.7251	1.06804	
740	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	Squared	22075.1	25775.1	1.16761	
740	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	Measured	5768.32	6434.78	1.11554	
741	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	Rooted	53.1114	56.7251	1.06804	
741	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	Measured	5768.32	6434.78	1.11554	
741	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [source:swissprot;acc:p22234]	Ranked	223.58	235.027	1.0512	
741	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Squared	23894.7	27894.5	1.16739	
742	brain protein 44. [source:swissprot;acc:o95563]	Ranked	126.215	120.078	1.05111	
742	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source:swissprot;acc:o75821]	Measured	4131.04	4607.9	1.11543	
742	homeobox protein engrailed-2 (hu-en-2). [source:swissprot;acc:p19622]	Squared	31406.6	36662.8	1.16736	
742	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Rooted	67.0234	71.5506	1.06755	
743	cpg binding protein (protein containing phd finger and cxxc domain 1). [source:swissprot;acc:q9p0u4]	Squared	31406.6	36662.8	1.16736	
743	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	Measured	4131.04	4607.9	1.11543	
743	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	Rooted	54.4988	51.0573	1.0674	
743	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Ranked	126.215	120.078	1.05111	
744	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [source:refseq;acc:nm_013375]	Squared	31406.6	36662.8	1.16736	
744	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Measured	12515.4	11221.1	1.11535	
744	dynactin 4. [source:refseq;acc:nm_032486]	Rooted	55.2242	51.7372	1.0674	
744	septin 6. [source:swissprot;acc:q14141]	Ranked	126.604	120.463	1.05098	
745	cytokine-like nuclear factor n-pac. [source:refseq;acc:nm_032569]	Squared	31406.6	36662.8	1.16736	
745	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	Measured	4086.6	4557.68	1.11527	
745	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	Ranked	214.679	225.568	1.05072	

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/