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 2268 to 2317 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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]	Divided	218.484	212.675	1.02731	
1135	homeobox protein engrailed-2 (hu-en-2). [source:swissprot;acc:p19622]	Subtracted	219.399	213.784	5.615	
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]	Divided	218.484	212.675	1.02731	
1136	cpg binding protein (protein containing phd finger and cxxc domain 1). [source:swissprot;acc:q9p0u4]	Subtracted	219.399	213.784	5.615	
1136	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Divided	218.484	212.675	1.02731	
1137	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [source:refseq;acc:nm_013375]	Subtracted	219.399	213.784	5.615	
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]	Divided	218.484	212.675	1.02731	
1138	cytokine-like nuclear factor n-pac. [source:refseq;acc:nm_032569]	Subtracted	219.399	213.784	5.615	
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]	Divided	218.484	212.675	1.02731	
1139	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	Divided	218.484	212.675	1.02731	
1139	transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	Subtracted	219.374	213.759	5.615	
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]	Divided	218.484	212.675	1.02731	
1140	hect type e3 ubiquitin ligase. [source:refseq;acc:nm_015052]	Subtracted	219.399	213.784	5.615	
1141	ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	Divided	218.484	212.675	1.02731	
1141	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	Subtracted	219.375	213.767	5.608	
1142	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [source:swissprot;acc:q9y2x7]	Subtracted	216.729	222.334	5.605	
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]	Divided	218.484	212.675	1.02731	
1143	kinesin protein. [source:refseq;acc:nm_032559]	Subtracted	224.858	219.264	5.594	
1143	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	Divided	218.484	212.675	1.02731	
1144	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Subtracted	135.844	130.259	5.585	
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]	Divided	218.484	212.675	1.02731	
1145	ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	Subtracted	224.805	219.251	5.554	
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]	Divided	218.481	212.675	1.0273	
1146	ubiquitin. [source:swissprot;acc:p02248]	Subtracted	209.061	203.518	5.543	
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]	Divided	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]	Divided	208.651	203.109	1.02729	
1147	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [source:swissprot;acc:o75381]	Subtracted	208.651	203.109	5.542	
1148	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	Subtracted	224.878	219.342	5.536	
1148	ubiquitin. [source:swissprot;acc:p02248]	Divided	209.061	203.518	1.02724	
1149	bystin. [source:swissprot;acc:q13895]	Divided	239.505	233.185	1.0271	
1149	kinesin-like protein kif2 (kinesin-2) (hk2). [source:swissprot;acc:o00139]	Subtracted	224.764	219.241	5.523	
1150	sorting nexin 1. [source:swissprot;acc:q13596]	Divided	209.868	215.522	1.02694	
1150	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [source:swissprot;acc:p27449]	Subtracted	218.186	212.672	5.514	
1151	metaxin 1. [source:swissprot;acc:q13505]	Divided	199.552	204.925	1.02693	
1151	sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	Subtracted	218.186	212.672	5.514	
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]	Divided	221.939	216.143	1.02682	
1152	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]	Subtracted	218.186	212.672	5.514	
1153	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	Subtracted	218.186	212.672	5.514	
1153	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	Divided	221.93	216.146	1.02676	
1154	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	Subtracted	218.186	212.672	5.514	
1154	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [source:swissprot;acc:q15181]	Divided	224.307	230.242	1.02646	
1155	inorganic pyrophosphatase 2 isoform 1. [source:refseq;acc:nm_176869]	Divided	224.307	230.242	1.02646	
1155	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	Subtracted	218.186	212.672	5.514	
1156	aryl-hydrocarbon interacting protein-like 1. [source:swissprot;acc:q9nzn9]	Divided	224.307	230.242	1.02646	
1156	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	Subtracted	218.186	212.672	5.514	
1157	ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [source:swissprot;acc:o00170]	Divided	224.307	230.242	1.02646	
1157	upstream binding protein 1 (lbp-1a). [source:refseq;acc:nm_014517]	Subtracted	220.742	215.237	5.505	
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]	Divided	221.877	216.167	1.02641	
1158	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Subtracted	220.742	215.237	5.505	
1159	lbp-9. [source:refseq;acc:nm_014553]	Subtracted	220.742	215.237	5.505	

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/