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 2208 to 2257 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1104	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]	Subtracted	218.484	212.675	5.809	
1105	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Divided	191.139	185.882	1.02828	
1105	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	Subtracted	218.484	212.675	5.809	
1106	pxr2b protein. [source:refseq;acc:nm_016559]	Divided	212.945	207.109	1.02818	
1106	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]	Subtracted	218.484	212.675	5.809	
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]	Divided	204.603	210.324	1.02796	
1107	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]	Subtracted	218.483	212.676	5.807	
1108	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Divided	218.006	212.119	1.02775	
1108	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]	Subtracted	218.481	212.675	5.806	
1109	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]	Subtracted	221.939	216.143	5.796	
1109	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Divided	218.098	212.209	1.02775	
1110	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	Divided	216.78	222.782	1.02769	
1110	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Subtracted	159.13	164.917	5.787	
1111	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Divided	217.99	212.123	1.02766	
1111	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	Subtracted	159.165	164.951	5.786	
1112	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	Subtracted	221.93	216.146	5.784	
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	Divided	251.863	258.829	1.02766	
1113	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	Divided	251.863	258.829	1.02766	
1113	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Subtracted	91.63	97.4011	5.7711	
1114	diphthamide biosynthesis-like protein 2. [source:refseq;acc:nm_001384]	Subtracted	227.274	233.041	5.767	
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	Divided	251.863	258.829	1.02766	
1115	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]	Subtracted	186.664	180.943	5.721	
1115	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	Divided	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]	Divided	251.863	258.829	1.02766	
1116	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]	Subtracted	204.603	210.324	5.721	
1117	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	Divided	168.989	164.46	1.02754	
1117	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	Subtracted	186.551	180.837	5.714	
1118	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]	Subtracted	221.877	216.167	5.71	
1118	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	Divided	168.995	164.467	1.02753	
1119	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]	Subtracted	207.553	213.256	5.703	
1119	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	Divided	218.528	212.676	1.02752	
1120	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Subtracted	186.741	181.041	5.7	
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]	Divided	218.528	212.676	1.02752	
1121	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Subtracted	187.834	182.137	5.697	
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]	Divided	218.529	212.676	1.02752	
1122	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	Subtracted	186.774	181.099	5.675	
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]	Divided	218.527	212.676	1.02751	
1123	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Subtracted	186.799	181.127	5.672	
1123	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	Divided	169.031	164.507	1.0275	
1124	kappa b-ras 1. [source:refseq;acc:nm_020345]	Subtracted	220.758	215.097	5.661	
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]	Divided	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]	Divided	204.404	210.022	1.02748	
1125	i-kappa-b-interacting ras-like protein 2. [source:refseq;acc:nm_017595]	Subtracted	220.758	215.097	5.661	
1126	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Divided	218.487	212.656	1.02742	
1126	snare associated protein snapin. [source:refseq;acc:nm_012437]	Subtracted	220.758	215.097	5.661	
1127	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	Divided	239.219	232.837	1.02741	
1127	sorting nexin 1. [source:swissprot;acc:q13596]	Subtracted	209.868	215.522	5.654	
1128	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Subtracted	187.96	182.308	5.652	
1128	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	Divided	221.286	215.399	1.02733	
1129	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	Divided	221.285	215.401	1.02732	

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/