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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4436 to 4485 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1109 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Ranked 218.098 212.209 1.02775
1110 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 222.782 1.02769
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Measured 5947.53 6481.56 1.08979
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Squared 25660.4 29342.7 1.1435
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Rooted 68.6067 72.0041 1.04952
1111 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Ranked 217.99 212.123 1.02766
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Rooted 68.4309 71.8158 1.04946
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Measured 6540.61 7127.41 1.08972
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Squared 59331.2 67833.7 1.14331
1112 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] Ranked 251.863 258.829 1.02766
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Rooted 68.4309 71.8157 1.04946
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Measured 5910.54 6440.58 1.08968
syntaxin 6. [swissprot;acc:o43752] Squared 26720.4 30548.3 1.14326
1113 growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Ranked 251.863 258.829 1.02766
myb-related protein a (a-myb). [swissprot;acc:p10243] Squared 22822.3 26090.1 1.14318
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Measured 5910.54 6440.58 1.08968
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Rooted 68.4466 71.8322 1.04946
1114 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Ranked 251.863 258.829 1.02766
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Measured 5910.54 6440.58 1.08968
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Rooted 68.2692 71.6429 1.04942
syntaxin 10 (syn10). [swissprot;acc:o60499] Squared 26702.8 30522.5 1.14304
1115 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Measured 5795.13 6314.19 1.08957
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Rooted 55.1167 57.8361 1.04934
hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Ranked 251.863 258.829 1.02766
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Squared 17475.6 19974.6 1.143
1116 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 27235.1 31125.2 1.14283
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Measured 5322.16 5798.38 1.08948
growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Ranked 251.863 258.829 1.02766
myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Rooted 55.1167 57.8361 1.04934
1117 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Measured 5322.16 5798.38 1.08948
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Squared 27234.2 31123.3 1.1428
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Rooted 55.1167 57.8361 1.04934
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Ranked 168.989 164.46 1.02754
1118 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Squared 27234.2 31123.3 1.1428
adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Measured 5322.16 5798.38 1.08948
nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Rooted 55.1167 57.8361 1.04934
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Ranked 168.995 164.467 1.02753
1119 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Measured 5322.16 5798.38 1.08948
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Squared 27234.2 31123.3 1.1428
myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Rooted 55.1167 57.8361 1.04934
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Ranked 218.528 212.676 1.02752
1120 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Squared 27233.3 31121.5 1.14277
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] Ranked 218.528 212.676 1.02752
heat shock factor binding protein 1. [swissprot;acc:o75506] Measured 5915.42 6443.77 1.08932
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Rooted 55.1167 57.8361 1.04934
1121 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Squared 24431.4 27918.1 1.14271
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Measured 4338.49 4725.86 1.08929
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Rooted 56.3761 59.1441 1.0491
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] Ranked 218.529 212.676 1.02752
1122 casein kinase i alpha s-like. [refseq;acc:nm_145203] Rooted 57.0994 59.9007 1.04906

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.
- http://analysis.yellowcouch.org/