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 1112 to 1161 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	251.863	258.829	1.02766	
1113	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	251.863	258.829	1.02766	
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	251.863	258.829	1.02766	
1115	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	251.863	258.829	1.02766	
1116	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [source:swissprot;acc:o75293]	251.863	258.829	1.02766	
1117	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	168.989	164.46	1.02754	
1118	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	168.995	164.467	1.02753	
1119	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	218.528	212.676	1.02752	
1120	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]	218.528	212.676	1.02752	
1121	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]	218.529	212.676	1.02752	
1122	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]	218.527	212.676	1.02751	
1123	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	169.031	164.507	1.0275	
1124	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [source:swissprot;acc:p30044]	207.553	213.256	1.02748	
1125	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	204.404	210.022	1.02748	
1126	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	218.487	212.656	1.02742	
1127	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	239.219	232.837	1.02741	
1128	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	221.286	215.399	1.02733	
1129	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	221.285	215.401	1.02732	
1130	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [source:swissprot;acc:q9uq80]	221.285	215.4	1.02732	
1131	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]	218.484	212.675	1.02731	
1132	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	218.484	212.675	1.02731	
1133	sec13-related protein. [source:swissprot;acc:p55735]	218.484	212.675	1.02731	
1134	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]	218.484	212.675	1.02731	
1135	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]	218.484	212.675	1.02731	
1136	yeast sec31p homolog. [source:refseq;acc:nm_014933]	218.484	212.675	1.02731	
1137	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]	218.484	212.675	1.02731	
1138	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]	218.484	212.675	1.02731	
1139	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	218.484	212.675	1.02731	
1140	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [source:refseq;acc:nm_005804]	218.484	212.675	1.02731	
1141	ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	218.484	212.675	1.02731	
1142	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [source:swissprot;acc:q9y5k8]	218.484	212.675	1.02731	
1143	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	218.484	212.675	1.02731	
1144	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [source:swissprot;acc:q9ui12]	218.484	212.675	1.02731	
1145	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]	218.481	212.675	1.0273	
1146	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [source:swissprot;acc:p15313]	218.483	212.676	1.0273	
1147	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [source:swissprot;acc:o75381]	208.651	203.109	1.02729	
1148	ubiquitin. [source:swissprot;acc:p02248]	209.061	203.518	1.02724	
1149	bystin. [source:swissprot;acc:q13895]	239.505	233.185	1.0271	
1150	sorting nexin 1. [source:swissprot;acc:q13596]	209.868	215.522	1.02694	
1151	metaxin 1. [source:swissprot;acc:q13505]	199.552	204.925	1.02693	
1152	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [source:refseq;acc:nm_139204]	221.939	216.143	1.02682	
1153	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	221.93	216.146	1.02676	
1154	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [source:swissprot;acc:q15181]	224.307	230.242	1.02646	
1155	inorganic pyrophosphatase 2 isoform 1. [source:refseq;acc:nm_176869]	224.307	230.242	1.02646	
1156	aryl-hydrocarbon interacting protein-like 1. [source:swissprot;acc:q9nzn9]	224.307	230.242	1.02646	
1157	ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [source:swissprot;acc:o00170]	224.307	230.242	1.02646	
1158	epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [source:refseq;acc:nm_022772]	221.877	216.167	1.02641	
1159	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	170.28	165.898	1.02641	
1160	2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	208.55	214.041	1.02633	
1161	kappa b-ras 1. [source:refseq;acc:nm_020345]	220.758	215.097	1.02632	

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/