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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison

Results: HTML CSV LaTeX

Showing element 1608 to 1657 of 3730 in total

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

Rank	description	green	red	network_comparison	
1106	pxr2b protein. [source:refseq;acc:nm_016559]	207.109	212.945	1.02818	
1107	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [source:swissprot;acc:o15270]	210.324	204.603	1.02796	
1108	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	212.119	218.006	1.02775	
1109	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	212.209	218.098	1.02775	
1110	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	222.782	216.78	1.02769	
1111	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	212.123	217.99	1.02766	
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	258.829	251.863	1.02766	
1113	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	258.829	251.863	1.02766	
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	258.829	251.863	1.02766	
1115	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	258.829	251.863	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]	258.829	251.863	1.02766	
1117	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	164.46	168.989	1.02754	
1118	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	164.467	168.995	1.02753	
1119	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	212.676	218.528	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]	212.676	218.528	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]	212.676	218.529	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]	212.676	218.527	1.02751	
1123	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	164.507	169.031	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]	213.256	207.553	1.02748	
1125	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	210.022	204.404	1.02748	
1126	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	212.656	218.487	1.02742	
1127	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	232.837	239.219	1.02741	
1128	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	215.399	221.286	1.02733	
1129	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	215.401	221.285	1.02732	
1130	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [source:swissprot;acc:q9uq80]	215.4	221.285	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]	212.675	218.484	1.02731	
1132	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	212.675	218.484	1.02731	
1133	sec13-related protein. [source:swissprot;acc:p55735]	212.675	218.484	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]	212.675	218.484	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]	212.675	218.484	1.02731	
1136	yeast sec31p homolog. [source:refseq;acc:nm_014933]	212.675	218.484	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]	212.675	218.484	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]	212.675	218.484	1.02731	
1139	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	212.675	218.484	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]	212.675	218.484	1.02731	
1141	ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	212.675	218.484	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]	212.675	218.484	1.02731	
1143	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	212.675	218.484	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]	212.675	218.484	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]	212.675	218.481	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]	212.676	218.483	1.0273	
1147	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [source:swissprot;acc:o75381]	203.109	208.651	1.02729	
1148	ubiquitin. [source:swissprot;acc:p02248]	203.518	209.061	1.02724	
1149	bystin. [source:swissprot;acc:q13895]	233.185	239.505	1.0271	
1150	sorting nexin 1. [source:swissprot;acc:q13596]	215.522	209.868	1.02694	
1151	metaxin 1. [source:swissprot;acc:q13505]	204.925	199.552	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]	216.143	221.939	1.02682	
1153	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	216.146	221.93	1.02676	
1154	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [source:swissprot;acc:q15181]	230.242	224.307	1.02646	
1155	inorganic pyrophosphatase 2 isoform 1. [source:refseq;acc:nm_176869]	230.242	224.307	1.02646	

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/