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 7762 to 7811 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
971 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Squared Divided 27478.1 31623.7 1.15087
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Measured 7813.36 8569.97 1.09684
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Squared Subtracted 20350.3 16816.1 3534.2
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Ranked 132.413 125.389 7.024
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Measured 5791.82 6340.86 549.04
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Rooted 61.8392 65.3085 3.4693
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Ranked Divided 211.987 204.964 1.03426
972 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Rooted 61.6649 65.1892 1.05715
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Measured 7813.48 8570.11 1.09684
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Subtracted 5791.82 6340.86 549.04
histone h4. [swissprot;acc:p02304] Squared 33111 29578.7 3532.3
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Ranked 132.413 125.389 7.024
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Divided 211.987 204.964 1.03426
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted Subtracted 61.8392 65.3085 3.4693
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Squared Divided 21083.8 24262 1.15074
973 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 20348.5 16817.2 3531.3
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Measured Divided 7810.11 8566.29 1.09682
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Ranked Subtracted 132.413 125.389 7.024
lbp-9. [refseq;acc:nm_014553] Rooted 61.8392 65.3085 3.4693
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Divided 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
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Measured Subtracted 5791.82 6340.86 549.04
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Ranked Divided 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
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Measured Subtracted 5791.82 6340.86 549.04
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] Divided 5365.06 5884.52 1.09682
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Ranked Subtracted 132.413 125.389 7.024
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Squared 26227.1 29756.6 3529.5
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Rooted 61.8392 65.3085 3.4693
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Divided 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 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Measured Subtracted 5791.82 6340.86 549.04
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] Divided 5365.14 5884.43 1.09679
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Ranked Subtracted 132.413 125.389 7.024
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Squared Divided 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
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Subtracted 61.9036 65.3694 3.4658
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Squared 26204.1 29732 3527.9
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 Divided 5365.22 5884.32 1.09675
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Rooted Subtracted 61.9121 65.373 3.4609
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] Squared 26204.1 29732 3527.9
lbp-9. [refseq;acc:nm_014553] Rooted Divided 61.8392 65.3085 1.0561
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Ranked Subtracted 132.413 125.389 7.024
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Squared Divided 27403.7 31533.7 1.15071
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Measured Subtracted 5791.82 6340.86 549.04
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Ranked Divided 243.34 235.322 1.03407
977 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 Subtracted 61.9129 65.3733 3.4604
annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Measured 5780.34 6329.3 548.96
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Ranked 211.987 204.964 7.023

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/