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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2912 to 2961 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
red
green
network_comparison
1456 EHD4 Divided eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] 207.024 211.086 1.01962
1457 no value Subtracted transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 215.328 211.267 4.061
EHD2 Divided eh-domain containing protein 2. [swissprot;acc:q9nzn4] 207.024 211.086 1.01962
1458 EHD1 Subtracted eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 211.085 4.061
EHD3 Divided eh-domain containing protein 3. [swissprot;acc:q9nzn3] 211.086 1.01962
1459 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 192.336 188.637 1.01961
RTN1 Subtracted reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 207.019 211.077 4.058
1460 SFRS10 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 4.056
TRIP12 Divided thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 205.817 209.851 1.0196
1461 MAPK11 Subtracted mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 171.231 167.177 4.054
RTN1 Divided reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 207.019 211.077 1.0196
1462 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 205.817 209.851
SPHK1 Subtracted sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 171.231 167.177 4.054
1463 no value Divided pnas-18. [sptrembl;acc:q9bzu3] 161.056 164.211 1.01959
DPAGT1 Subtracted udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] 171.231 167.177 4.054
1464 no value Divided poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 217.351 213.18 1.01957
DLC1 Subtracted rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] 171.231 167.177 4.054
1465 MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
MTO1 Divided mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 217.351 213.18 1.01957
1466 CHRNA6 Subtracted neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 171.231 167.177 4.054
RTN2 Divided reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] 207.022 211.073 1.01957
1467 ISCU Subtracted nitrogen fixation cluster-like. [refseq;acc:nm_014301] 171.231 167.177 4.054
MPP2 Divided maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 228.513 232.983 1.01956
1468 DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 212.001 207.937 1.01954
STARD13 Subtracted star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 171.231 167.177 4.054
1469 RTN3 Divided reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 207.013 211.05 1.0195
STARD8 Subtracted star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 171.231 167.177 4.054
1470 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
QARS Divided glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 221.412 217.199 1.0194
1471 MAPKAPK3 Subtracted mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 171.231 167.177 4.054
SRM Divided spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] 221.412 217.199 1.0194
1472 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
MAPK14 Subtracted 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] 171.231 167.177 4.054
1473 CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]
EARS2 Divided glutamyl trna synthetase. [sptrembl;acc:o14563] 221.412 217.199 1.0194
1474 CHRNA3 Subtracted neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 171.231 167.177 4.054
RANBP5 Divided importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 218.582 214.427 1.01938
1475 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 181.882 178.438 1.0193
SPHK2 Subtracted sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 171.231 167.177 4.054
1476 RANBP6 Divided ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 218.591 214.457 1.01928
RTN2 Subtracted reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] 207.022 211.073 4.051
1477 no value Divided transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 215.328 211.267 1.01922
RTN3 Subtracted reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 207.013 211.05 4.037
1478 SFRS10 Divided 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 1.01922
TRIP12 Subtracted thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 205.817 209.851 4.034
1479 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]
MPP6 Divided maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] 228.469 232.855 1.0192
1480 CPSF6 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
MAP3K7 Subtracted 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] 213.251 209.264 3.987
1481 ACTR1A alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 225.148 221.177 3.971

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
- Hugo is the HGNC identifier if it exists
- 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/