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 2610 to 2659 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1305 serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] High confidence 218.439 213.436 1.02344
1306 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Low confidence 199.275 194.918 1.02235
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] High confidence 218.441 213.441 1.02343
1307 myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613] Low confidence 204.064 199.602 1.02235
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] High confidence 218.44 213.44 1.02343
1308 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Low confidence 199.268 194.914 1.02234
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] High confidence 218.44 213.439 1.02343
1309 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 226.439 221.26 1.02341
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Low confidence 200.536 196.157 1.02232
1310 p66 alpha. [refseq;acc:nm_017660] 229.478 224.473 1.0223
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] High confidence 226.439 221.26 1.02341
1311 transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Low confidence 229.478 224.473 1.0223
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] High confidence 226.439 221.26 1.02341
1312 rad50 homolog isoform 1. [refseq;acc:nm_005732] 199.739 204.407 1.02337
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Low confidence 229.478 224.473 1.0223
1313 serologically defined colon cancer antigen 1. [refseq;acc:nm_004713] 202.396 197.985 1.02228
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] High confidence 222.573 227.75 1.02326
1314 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Low confidence 201.948 197.549 1.02227
signal transducer and activator of transcription 4. [swissprot;acc:q14765] High confidence 222.573 227.751 1.02326
1315 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Low confidence 206.697 202.196 1.02226
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] High confidence 222.574 227.752 1.02326
1316 schwannomin interacting protein 1. [refseq;acc:nm_014575] Low confidence 201.232 196.85 1.02226
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] High confidence 222.569 227.739 1.02323
1317 cbf1 interacting corepressor. [refseq;acc:nm_004882] Low confidence 203.649 199.217 1.02225
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] High confidence 206.773 202.105 1.0231
1318 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Low confidence 203.649 199.217 1.02225
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] High confidence 222.546 227.673 1.02304
1319 fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648] Low confidence 208.606 213.247 1.02225
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] High confidence 159.75 156.153 1.02304
1320 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] Low confidence 200.171 195.819 1.02222
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] High confidence 222.544 227.667 1.02302
1321 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Low confidence 199.938 195.591 1.02222
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] High confidence 226.347 221.259 1.023
1322 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Low confidence 198.322 194.014 1.0222
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] High confidence 159.86 156.275 1.02294
1323 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 205.225 200.625 1.02293
neuronal guanine nucleotide exchange factor. [refseq;acc:nm_019850] Low confidence 203.926 199.498 1.0222
1324 beta-galactosidase precursor (ec 3.2.1.23) (lactase) (acid beta- galactosidase). [swissprot;acc:p16278] 203.758 199.335 1.02219
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] High confidence 159.993 156.421 1.02284
1325 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Low confidence 201.909 197.526 1.02219
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] High confidence 217.133 212.289 1.02282
1326 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 213.648 1.02275
pre-mrna splicing factor atp-dependent rna helicase prp16 (atp- dependent rna helicase ddx38) (deah-box protein 38). [swissprot;acc:q92620] Low confidence 202.039 197.654 1.02219
1327 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 201.908 197.525
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] High confidence 218.509 213.648 1.02275
1328 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Low confidence 198.342 194.038 1.02218
calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] High confidence 218.509 213.649 1.02275
1329 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 187.586 183.516 1.02218
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] High confidence 218.509 213.648 1.02275
1330 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 218.508

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/