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 2930 to 2979 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1465 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Divided 217.351 213.18 1.01957
1466 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Subtracted 171.231 167.177 4.054
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Divided 207.022 211.073 1.01957
1467 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 228.513 232.983 1.01956
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Subtracted 171.231 167.177 4.054
1468 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Divided 212.001 207.937 1.01954
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Subtracted 171.231 167.177 4.054
1469 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Divided 207.013 211.05 1.0195
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 171.231 167.177 4.054
1470 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Divided 221.412 217.199 1.0194
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Subtracted 171.231 167.177 4.054
1471 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Divided 221.412 217.199 1.0194
1472 glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Subtracted 171.231 167.177 4.054
1473 glutamyl trna synthetase. [sptrembl;acc:o14563] Divided 221.412 217.199 1.0194
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Subtracted 171.231 167.177 4.054
1474 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Divided 218.582 214.427 1.01938
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 171.231 167.177 4.054
1475 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided 181.882 178.438 1.0193
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Subtracted 171.231 167.177 4.054
1476 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Divided 218.591 214.457 1.01928
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Subtracted 207.022 211.073 4.051
1477 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 207.013 211.05 4.037
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Divided 215.328 211.267 1.01922
1478 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 215.122 211.066
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Subtracted 205.817 209.851 4.034
1479 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Divided 228.469 232.855 1.0192
1480 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 218.664 214.55 1.01918
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Subtracted 213.251 209.264 3.987
1481 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 225.148 221.177 3.971
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided 208.432 204.516 1.01915
1482 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Subtracted 225.148 221.177 3.971
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Divided 224.354 220.15 1.0191
1483 pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 198.927 202.726
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Subtracted 228.419 232.376 3.957
1484 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Divided 198.927 202.726 1.0191
cytochrome c. [swissprot;acc:p00001] Subtracted 228.419 232.376 3.957
1485 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 207.877 203.989 1.01906
1486 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Subtracted 228.419 232.376 3.957
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Divided 207.877 203.989 1.01906
1487 fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Subtracted 228.419 232.376 3.957
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Divided 207.877 203.989 1.01906
1488 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Subtracted 228.419 232.376 3.957
1489 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Divided 213.251 209.264 1.01905
1490 protein cgi-147. [swissprot;acc:q9y3e5] 221.961 226.186 1.01903

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/