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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 3708 to 3757 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
927	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	Rooted	62.0422	65.7019	1.05899	
928	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	Measured	5638.46	6194.04	1.09853	
928	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	Rooted	62.0422	65.7019	1.05899	
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Ranked	225.976	218.017	1.03651	
928	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Squared	20685.1	23904.8	1.15565	
929	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	Ranked	225.955	218.015	1.03642	
929	surfeit locus protein 1. [source:swissprot;acc:q15526]	Measured	5638.46	6194.04	1.09853	
929	tubulin-tyrosine ligase. [source:refseq;acc:nm_153712]	Squared	22626.3	26143	1.15543	
929	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). [source:swissprot;acc:o95670]	Rooted	62.3617	66.0327	1.05887	
930	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	Rooted	62.3617	66.0327	1.05887	
930	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Measured	5638.65	6194.23	1.09853	
930	homolog of yeast maf1. [source:refseq;acc:nm_032272]	Squared	26029.5	30074.5	1.1554	
930	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [source:swissprot;acc:p14618]	Ranked	231.357	239.778	1.0364	
931	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Ranked	159.13	164.917	1.03637	
931	sec13-related protein. [source:swissprot;acc:p55735]	Rooted	62.3618	66.0328	1.05887	
931	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	Measured	5638.59	6194.17	1.09853	
931	tumor differentially expressed protein 2. [source:refseq;acc:nm_178865]	Squared	26029.5	30074.5	1.1554	
932	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	Measured	5638.46	6194.04	1.09853	
932	mitochondrial translational release factor 1-like. [source:refseq;acc:nm_019041]	Ranked	225.939	218.013	1.03636	
932	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [source:swissprot;acc:q13530]	Squared	26029.5	30074.5	1.1554	
932	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [source:swissprot;acc:q96lb4]	Rooted	62.3617	66.0327	1.05887	
933	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	Ranked	159.165	164.951	1.03635	
933	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	Measured	5638.46	6194.04	1.09853	
933	tumor differentially expressed 1 protein like. [source:swissprot;acc:q9nrx5]	Squared	26029.5	30074.5	1.1554	
933	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [source:swissprot;acc:p21281]	Rooted	62.3618	66.0328	1.05887	
934	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [source:swissprot;acc:o43175]	Squared	26029.5	30074.5	1.1554	
934	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	Ranked	242.024	233.544	1.03631	
934	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Rooted	62.3618	66.0328	1.05887	
934	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [source:swissprot;acc:o14874]	Measured	5640	6195.52	1.0985	
935	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	Squared	15461.1	17854.3	1.15479	
935	neurotrimin precursor (hnt). [source:swissprot;acc:q9p121]	Measured	5413.63	5946.46	1.09842	
935	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	Ranked	232.473	224.372	1.03611	
935	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [source:swissprot;acc:o75348]	Rooted	62.3617	66.0327	1.05887	
936	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	Ranked	232.473	224.372	1.03611	
936	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Measured	5628.21	6180.37	1.09811	
936	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Squared	15461.1	17854.3	1.15479	
936	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [source:swissprot;acc:p36543]	Rooted	62.3618	66.0328	1.05887	
937	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14409]	Squared	25043.9	28914	1.15453	
937	nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	Measured	5859.25	6432.03	1.09776	
937	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	Ranked	220.246	212.618	1.03588	
937	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]	Rooted	62.3588	66.0297	1.05887	
938	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Measured	5859.25	6432.03	1.09776	
938	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	Rooted	62.3618	66.0328	1.05887	
938	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:p32189]	Squared	25043.4	28913.4	1.15453	
938	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	Ranked	220.246	212.618	1.03588	
939	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	Ranked	216.501	224.27	1.03588	
939	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [source:refseq;acc:nm_005804]	Rooted	62.3617	66.0327	1.05887	
939	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14410]	Squared	25044.9	28915.2	1.15453	
939	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	Measured	5859.25	6432.03	1.09776	
940	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	Measured	5568.96	6113.35	1.09775	

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/