MK5 Microarray Data

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

Results: HTML CSV LaTeX

Showing element 1100 to 1149 of 3228 in total

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

Rank	description	green	network_comparison	red
1100	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194]	203.183	1.02889	209.052
1101	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	226.584	1.02857	220.291
1102	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	235.974	1.02847	229.442
1103	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	235.972	1.02846	229.441
1104	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8]	238.486	1.0283	231.922
1105	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109]	185.882	1.02828	191.139
1106	pxr2b protein. [refseq;acc:nm_016559]	207.109	1.02818	212.945
1107	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270]	210.324	1.02796	204.603
1108	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167]	212.119	1.02775	218.006
1109	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	212.209		218.098
1110	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161]	222.782	1.02769	216.78
1111	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	212.123	1.02766	217.99
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	258.829		251.863
1113	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
1115	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]
1116	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]
1117	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	164.46	1.02754	168.989
1118	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	164.467	1.02753	168.995
1119	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	212.676	1.02752	218.528
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). [refseq;acc:nm_020632]
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). [swissprot;acc:q93050]			218.529
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). [swissprot;acc:q13488]		1.02751	218.527
1123	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	164.507	1.0275	169.031
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). [swissprot;acc:p30044]	213.256	1.02748	207.553
1125	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	210.022		204.404
1126	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	212.656	1.02742	218.487
1127	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	232.837	1.02741	239.219
1128	homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	215.399	1.02733	221.286
1129	homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	215.401	1.02732	221.285
1130	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80]	215.4
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). [swissprot;acc:o95670]	212.675	1.02731	218.484
1132	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
1133	sec13-related protein. [swissprot;acc:p55735]
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). [swissprot;acc:q96lb4]
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). [swissprot;acc:p21281]
1136	yeast sec31p homolog. [refseq;acc:nm_014933]
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). [swissprot;acc:o75348]
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). [swissprot;acc:p36543]
1139	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]
1140	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]
1141	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]
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). [swissprot;acc:q9y5k8]
1143	secretory pathway component sec31b-1. [refseq;acc:nm_015490]
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). [swissprot;acc:q9ui12]
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). [swissprot;acc:q16864]		1.0273	218.481
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). [swissprot;acc:p15313]	212.676		218.483
1147	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381]	203.109	1.02729	208.651
1148	ubiquitin. [swissprot;acc:p02248]	203.518	1.02724	209.061
1149	bystin. [swissprot;acc:q13895]	233.185	1.0271	239.505

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.