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 12164 to 12213 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1019 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Rooted Divided 60.7786 64.0257 1.05343
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Measured Subtracted 5704 6241.36 537.36
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Squared 17281.7 20723 3441.3
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Divided 22827.7 26208.2 1.14809
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Ranked 221.302 214.409 1.03215
1020 40s ribosomal protein s28. [swissprot;acc:p25112] Rooted Subtracted 70.4215 73.7627 3.3412
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Measured Divided 5791.82 6340.86 1.0948
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Squared 26499.7 30423.6 1.14807
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Ranked 221.28 214.409 1.03205
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Rooted 60.7802 64.0247 1.05338
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Squared Subtracted 21455.4 24895.7 3440.3
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Measured 7234.61 7771.58 536.97
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Ranked 226.218 232.88 6.662
1021 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] Divided 221.278 214.409 1.03204
block 23. [sptrembl;acc:q8nhw5] Subtracted 226.205 232.858 6.653
endothelial-derived gene 1. [refseq;acc:nm_025205] Squared 26062.8 29502.8 3440
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Rooted 62.0618 65.4025 3.3407
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Measured 7234.61 7771.58 536.97
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Rooted Divided 60.9994 57.9085 1.05338
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Measured 5791.82 6340.86 1.0948
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Squared 26499.7 30423.6 1.14807
1022 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Ranked Subtracted 226.203 232.855 6.652
adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] Squared Divided 26499.7 30423.6 1.14807
alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] Subtracted 44474.9 41050.1 3424.8
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Ranked Divided 205.632 199.266 1.03195
elks protein. [refseq;acc:nm_015064] Rooted Subtracted 62.0618 65.4025 3.3407
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Divided 53.4366 56.2771 1.05316
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Measured 6435.94 7045.75 1.09475
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Subtracted 6783.78 7320.39 536.61
1023 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 7232.14 7768.35 536.21
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Rooted Divided 60.7905 64.0183 1.0531
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Ranked Subtracted 202.027 195.386 6.641
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Squared Divided 16630.6 19092.9 1.14806
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Rooted Subtracted 61.5654 64.9046 3.3392
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Measured Divided 6435.02 7044.65 1.09474
transforming protein rhoc (h9). [swissprot;acc:p08134] Ranked 205.632 199.266 1.03195
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Squared Subtracted 21175.9 24598.1 3422.2
1024 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Measured Divided 5706.5 6245.55 1.09446
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Ranked Subtracted 203.381 196.76 6.621
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Rooted Divided 48.9418 51.5408 1.0531
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Subtracted 64.2202 67.5585 3.3383
orphan nuclear receptor tr2. [swissprot;acc:p13056] Squared Divided 29904.9 34332.5 1.14806
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Ranked 205.632 199.266 1.03195
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Measured Subtracted 4725.28 5261.06 535.78
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Squared 18240.1 21659.2 3419.1
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Ranked Divided 205.632 199.266 1.03195
40s ribosomal protein s30. [swissprot;acc:q05472] Subtracted 223.44 216.875 6.565
Rooted 61.3513 64.6874 3.3361
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Divided 55.3631 58.2965 1.05298
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Squared 22126.7 25398.5 1.14787

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/