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 3886 to 3935 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
972 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Measured 7813.48 8570.11 1.09684
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Ranked 211.987 204.964 1.03426
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Squared 21083.8 24262 1.15074
973 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Measured 7810.11 8566.29 1.09682
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Rooted 49.307 52.1123 1.05689
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Squared 27404 31534 1.15071
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Ranked 211.987 204.964 1.03426
974 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] Squared 27403.4 31533.3 1.15071
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Measured 5365.06 5884.52 1.09682
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Rooted 61.8392 65.3085 1.0561
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Ranked 211.987 204.964 1.03426
975 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Measured 5365.14 5884.43 1.09679
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Squared 27403.4 31533.3 1.15071
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Ranked 211.987 204.964 1.03426
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted 61.8392 65.3085 1.0561
976 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Measured 5365.22 5884.32 1.09675
lbp-9. [refseq;acc:nm_014553] Rooted 61.8392 65.3085 1.0561
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Squared 27403.7 31533.7 1.15071
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Ranked 243.34 235.322 1.03407
977 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 228.953 221.421 1.03402
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Rooted 61.8392 65.3085 1.0561
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Measured 4115.9 4513.14 1.09651
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] Squared 27402.5 31532.3 1.15071
978 disrupter of silencing 10. [refseq;acc:nm_020368] 27403.4 31533.3
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Ranked 228.953 221.421 1.03402
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Rooted 61.9036 65.3694 1.05599
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Measured 6654.42 7296.51 1.09649
979 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Rooted 67.7212 71.51 1.05595
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Ranked 202.027 195.386 1.03399
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Squared 27403.4 31533.4 1.15071
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Measured 6654.42 7296.51 1.09649
980 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Ranked 130.289 134.713 1.03396
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Rooted 61.9121 65.373 1.0559
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Squared 27403.6 31533.6 1.15071
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Measured 6654.42 7296.51 1.09649
981 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Rooted 61.9129 65.3733 1.05589
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Measured 6654.42 7296.51 1.09649
exocyst complex component sec6. [swissprot;acc:o60645] Ranked 207.186 200.398 1.03387
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Squared 27403.1 31533 1.15071
982 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Measured 6654.42 7296.51 1.09649
bystin. [swissprot;acc:q13895] Rooted 53.1515 56.1209 1.05587
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Ranked 243.312 235.351 1.03383
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Squared 30999.6 35666.3 1.15054
983 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Rooted 56.1832 53.2244 1.05559
pbk1 protein. [sptrembl;acc:o76021] Ranked 243.312 235.353 1.03382
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Squared 31010.8 35677.6 1.15049
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Measured 6654.42 7296.51 1.09649
984 bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Rooted 56.1854 53.2272 1.05558
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Measured 6362.64 6976.1 1.09642
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Ranked 116.71 120.654 1.03379

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/