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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 8191 to 8240 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
Value Type
description
red
network_comparison
green
1024 Subtracted LSM8 Squared u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 18240.1 3419.1 21659.2
PAPD5 Measured topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] 4725.28 535.78 5261.06
1025 Divided CASP7 Rooted caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 55.3631 1.05298 58.2965
MPST Ranked 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 205.632 1.03195 199.266
PMM2 Measured phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 5511.96 1.09434 6031.95
PPA1 Squared inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 22126.7 1.14787 25398.5
Subtracted FAU Ranked 40s ribosomal protein s30. [swissprot;acc:q05472] 223.44 6.565 216.875
Rooted 61.3513 3.3361 64.6874
FDXR Measured nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 5947.53 534.03 6481.56
PRPF19 Squared nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 21095.7 3411.8 24507.5
1026 Divided CASP3 Rooted apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] 55.3631 1.05298 58.2965
PMM1 Measured phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 5509.89 1.09427 6029.29
PPA2 Squared inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] 22126.7 1.14787 25398.5
RHOA Ranked transforming protein rhoa (h12). [swissprot;acc:p06749] 205.632 1.03195 199.266
Subtracted HAO1 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] 231.922 6.564 238.486
LSAMP Measured limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 5396.36 533.05 5929.41
SETMAR Rooted set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 54.765 3.3331 51.4319
TPI1 Squared triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 19970 3396.8 23366.8
1027 Divided AIPL1 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] 22126.7 1.14787 25398.5
CYC1 Rooted cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 52.1219 1.05294 49.5013
MAT2A Measured s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 6123.15 1.09422 6700.05
SUCLG1 Ranked succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] 211.908 1.03171 218.627
Subtracted no value adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 211.449 6.549 217.998
Squared tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] 30900.2 3394.7 34294.9
CLEC4M Rooted cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 54.765 3.3331 51.4319
OPCML Measured opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 5406.5 532.92 5939.42
1028 Divided AIP Squared ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] 22126.7 1.14787 25398.5
ARHGAP26 Rooted oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 52.1219 1.05294 49.5013
QPRT Measured nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] 5704 1.09421 6241.36
SUCLA2 Ranked succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] 211.908 1.03171 218.627
Subtracted no value Measured neurotrimin precursor (hnt). [swissprot;acc:q9p121] 5413.63 532.83 5946.46
FCER2 Rooted low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 54.765 3.3331 51.4319
GPD1 Squared glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 23321.3 3394.1 26715.4
HSD17B1 Ranked estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 211.449 6.549 217.998
1029 Divided CTNNB1 Measured beta-catenin (pro2286). [swissprot;acc:p35222] 5635.26 1.0942 6166.09
DDB1 Ranked dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 222.364 1.03168 215.535
FTHL17 Squared ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 31999.3 1.14774 36726.8
RGN Rooted senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 52.1219 1.05294 49.5013
Subtracted no value Ranked 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 211.449 6.549 217.998
CD209 Rooted cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 54.765 3.3331 51.4319
KHK Squared ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] 22569.9 3386.7 25956.6
POLS Measured polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 4726.38 532.57 5258.95
1030 Divided no value casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 5048.33 1.09419 5523.85
FTMT Squared mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 31994.3 1.1477 36720
OPHN1 Rooted oligophrenin 1. [swissprot;acc:o60890] 52.1219 1.05294 49.5013
PCCB Ranked propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] 222.364 1.03168 215.535
Subtracted no value Squared purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 22569.9 3386.7 25956.6
C15orf15 Rooted ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 70.4902 3.3309 73.8211
ETFA Measured electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 7919.76 532.25 8452.01
RDH8 Ranked retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] 211.449 6.549 217.998

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/