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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2200 to 2249 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
1100 ATP2C1 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] High confidence 209.052 203.183 1.02889
1101 EPHB6 ephrin type-b receptor 6 precursor (tyrosine-protein kinase-defective receptor eph-6) (hep). [swissprot;acc:o15197] Low confidence 210.722 205.826 1.02379
KARS lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] High confidence 220.291 226.584 1.02857
1102 no value 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 235.974 1.02847
EPHA8 ephrin type-a receptor 8 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor eek) (eph-and elk-related kinase) (hek3). [swissprot;acc:p29322] Low confidence 210.722 205.826 1.02379
1103 EPHA3 ephrin type-a receptor 3 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor etk1) (hek) (hek4). [swissprot;acc:p29320]
RPS27L ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] High confidence 229.441 235.972 1.02846
1104 FZD8 frizzled 8 precursor (frizzled-8) (fz-8) (hfz8). [swissprot;acc:q9h461] Low confidence 206.584 201.786 1.02378
HAO1 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] High confidence 231.922 238.486 1.0283
1105 FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 191.139 185.882 1.02828
TRIB2 tribbles homolog 2. [refseq;acc:nm_021643] Low confidence 203.515 198.787 1.02378
1106 no value mitochondrial carrier protein mgc4399. [refseq;acc:nm_032315] 201.02 196.352 1.02377
PEX5L pxr2b protein. [refseq;acc:nm_016559] High confidence 212.945 207.109 1.02818
1107 RHCG rh type c glycoprotein. [refseq;acc:nm_016321] Low confidence 201.221 196.55 1.02376
SPTLC2 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] High confidence 204.603 210.324 1.02796
1108 FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 1.02775
VAPB vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292] Low confidence 204.27 199.529 1.02376
1109 MAPK13 mitogen-activated protein kinase 13 (ec 2.7.1.37) (stress-activated protein kinase-4) (mitogen-activated protein kinase p38 delta) (map kinase p38 delta). [swissprot;acc:o15264] 200.443 195.793 1.02375
TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] High confidence 218.098 212.209 1.02775
1110 GIT2 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 222.782 1.02769
LBR lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Low confidence 201.984 197.299 1.02375
1111 no value apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] High confidence 217.99 212.123 1.02766
TM7SF2 delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Low confidence 202.004 197.323 1.02372
1112 HNF4G hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] High confidence 251.863 258.829 1.02766
VAPA vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0] Low confidence 204.256 199.524 1.02372
1113 CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 200.326 195.686 1.02371
GADD45G growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] High confidence 251.863 258.829 1.02766
1114 GADD45A growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
SLC7A3 solute carrier family 7 (cationic amino acid transporter, y+ system), member 3. [refseq;acc:nm_032803] Low confidence 200.679 196.033 1.0237
1115 HNF4A hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] High confidence 251.863 258.829 1.02766
SLC7A2 low-affinity cationic amino acid transporter-2 (cat-2) (cat2). [swissprot;acc:p52569] Low confidence 200.679 196.033 1.0237
1116 DUS1L pp3111 protein. [refseq;acc:nm_022156] 203.007 198.316 1.02365
GADD45B growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] High confidence 251.863 258.829 1.02766
1117 NUCB1 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Low confidence 211.871 216.875 1.02362
NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] High confidence 168.989 164.46 1.02754
1118 NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 168.995 164.467 1.02753
SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425] Low confidence 187.49 183.168 1.0236
1119 ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] High confidence 218.528 212.676 1.02752
BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Low confidence 201.761 197.111 1.02359
1120 ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] 201.621 196.976 1.02358
ATP6V0A4 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] High confidence 218.528 212.676 1.02752
1121 ATP6V0A1 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
RHBG rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Low confidence 201.247 196.611 1.02358
1122 ATP6V1E1 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] 201.537 196.894
TCIRG1 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] High confidence 218.527 212.676 1.02751
1123 ATP6V1A vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Low confidence 201.621 196.976 1.02358
NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] High confidence 169.031 164.507 1.0275
1124 NPEPPS puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Low confidence 201.395 196.76 1.02356
PRDX5 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] High confidence 207.553 213.256 1.02748
1125 no value dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 204.404 210.022

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
- Hugo is the HGNC identifier if it exists
- 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/