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 4408 to 4457 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1102 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Measured 5462.88 5958.12 1.09066
1103 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Rooted 61.5152 64.5623 1.04953
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Measured 5358.18 5843.73 1.09062
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Squared 19147.7 21914.4 1.14449
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Ranked 229.441 235.972 1.02846
1104 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Rooted 61.5152 64.5623 1.04953
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Squared 24175.6 27657.3 1.14402
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Ranked 231.922 238.486 1.0283
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Measured 5359.72 5844.97 1.09054
1105 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Ranked 191.139 185.882 1.02828
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Rooted 61.5152 64.5623 1.04953
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Squared 24175.6 27657.3 1.14402
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Measured 5460.49 5954.62 1.09049
1106 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Rooted 61.5152 64.5623 1.04953
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Squared 24175.6 27657.3 1.14402
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Measured 5489.99 5986.63 1.09046
pxr2b protein. [refseq;acc:nm_016559] Ranked 212.945 207.109 1.02818
1107 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Rooted 61.5152 64.5623 1.04953
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Squared 24175.6 27657.3 1.14402
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Measured 5489.99 5986.63 1.09046
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] Ranked 204.603 210.324 1.02796
1108 flotillin-1. [swissprot;acc:o75955] Rooted 61.5152 64.5623 1.04953
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Ranked 218.006 212.119 1.02775
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Squared 24175.6 27657.3 1.14402
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Measured 4846.16 5283.08 1.09016
1109 myb-related protein b (b-myb). [swissprot;acc:p10244] Squared 22817.9 26093.4 1.14355
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Measured 6545.19 7132.89 1.08979
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Rooted 61.5152 64.5622 1.04953
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

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/