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 5858 to 5907 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1465 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Subtracted High confidence 171.231 167.177 4.054
mitogen-activated protein kinase kinase kinase 2 (ec 2.7.1.-) (mapk/erk kinase kinase 2) (mek kinase 2) (mekk 2). [swissprot;acc:q9y2u5] Divided Low confidence 197.06 192.901 1.02156
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] High confidence 217.351 213.18 1.01957
1466 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted Low confidence 202.583 198.329 4.254
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] High confidence 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
vesicle trafficking protein sec22b. [refseq;acc:nm_004892] Low confidence 202.483 198.21 1.02156
1467 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 205.917 201.572
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] High confidence 228.513 232.983 1.01956
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Subtracted Low confidence 200.812 196.561 4.251
nitrogen fixation cluster-like. [refseq;acc:nm_014301] High confidence 171.231 167.177 4.054
1468 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Low confidence 199.817 195.566 4.251
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Divided High confidence 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
vinculin (metavinculin). [swissprot;acc:p18206] Divided Low confidence 202.572 198.298 1.02155
1469 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Subtracted 203.641 199.39 4.251
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Divided High confidence 207.013 211.05 1.0195
retinoic acid receptor rxr-alpha. [swissprot;acc:p19793] Low confidence 203.215 198.93 1.02154
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted High confidence 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
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Subtracted Low confidence 192.905 188.658 4.247
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] High confidence 171.231 167.177 4.054
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Divided Low confidence 200.929 196.693 1.02154
1471 dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] 203.488 199.197
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Subtracted 192.956 188.71 4.246
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] High confidence 171.231 167.177 4.054
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Divided 221.412 217.199 1.0194
1472 ceramide glucosyltransferase (ec 2.4.1.80) (glucosylceramide synthase) (gcs) (udp-glucose:n-acylsphingosine d-glucosyltransferase) (glct-1). [swissprot;acc:q16739] Subtracted Low confidence 192.933 188.687 4.246
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Divided High confidence 221.412 217.199 1.0194
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
ubiquitously transcribed x chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the x chromosome). [swissprot;acc:o15550] Divided Low confidence 200.93 196.694 1.02154
1473 glutamyl trna synthetase. [sptrembl;acc:o14563] High confidence 221.412 217.199 1.0194
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Subtracted 171.231 167.177 4.054
ptd016 protein. [refseq;acc:nm_016125] Divided Low confidence 203.488 199.197 1.02154
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 199.796 195.55 4.246
1474 elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Divided 202.941 198.663 1.02153
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] High confidence 218.582 214.427 1.01938
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 171.231 167.177 4.054
vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034] Low confidence 200.787 196.542 4.245
1475 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 202.722 198.48 4.242
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided High confidence 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
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Divided Low confidence 198.197 194.02 1.02153
1476 eyes absent homolog 1. [swissprot;acc:q99502] 203.162 198.88
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Subtracted 203.549 199.307 4.242
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Divided High confidence 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 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Low confidence 202.972 198.731 4.241
hn1 like. [refseq;acc:nm_144570] Divided 190.569 186.552 1.02153
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Subtracted High confidence 207.013 211.05 4.037

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/