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 1951 to 2000 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
976 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Low confidence 200.046 195.23 1.02467
t-cell activation wd repeat protein. [refseq;acc:nm_139281] High confidence 243.34 235.322 1.03407
977 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 228.953 221.421 1.03402
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Low confidence 200.046 195.231 1.02466
978 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 201.137 196.296
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] High confidence 228.953 221.421 1.03402
979 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] 202.027 195.386 1.03399
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Low confidence 196.475 191.748 1.02465
980 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] High confidence 130.289 134.713 1.03396
iap-associated factor viaf1; phosducin-like 2. [refseq;acc:nm_024065] Low confidence 201.185 196.346 1.02465
981 exocyst complex component sec6. [swissprot;acc:o60645] High confidence 207.186 200.398 1.03387
williams beuren syndrome chromosome region 21 isoform 1. [refseq;acc:nm_148912] Low confidence 201.186 196.347 1.02465
982 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] High confidence 243.312 235.351 1.03383
ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995] Low confidence 204.318 199.402 1.02465
983 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 201.215 196.378 1.02463
pbk1 protein. [sptrembl;acc:o76021] High confidence 243.312 235.353 1.03382
984 lysosomal protective protein precursor (ec 3.4.16.5) (cathepsin a) (carboxypeptidase c) (protective protein for beta-galactosidase). [swissprot;acc:p10619] Low confidence 201.065 196.232 1.02463
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] High confidence 116.71 120.654 1.03379
985 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 151.012 154.728 1.02461
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] High confidence 233.402 225.782 1.03375
986 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Low confidence 192.111 187.496 1.02461
exocyst complex component sec5. [swissprot;acc:q96kp1] High confidence 116.771 120.707 1.03371
987 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 218.459 211.338 1.03369
wd-repeat protein an11 homolog. [swissprot;acc:o15491] Low confidence 200.981 196.157 1.02459
988 alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] 186.556 182.079
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] High confidence 218.461 211.343 1.03368
989 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Low confidence 207.083 202.115 1.02458
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] High confidence 218.462 211.345 1.03367
990 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 243.297 235.373
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Low confidence 200.345 195.539 1.02458
991 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] High confidence 203.381 196.76 1.03365
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Low confidence 203.123 198.251 1.02457
992 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] High confidence 218.468 211.357 1.03364
ubiquitin-conjugating enzyme e2 c (ec 6.3.2.19) (ubiquitin-protein ligase c) (ubiquitin carrier protein c) (ubch10). [swissprot;acc:o00762] Low confidence 204.364 199.464 1.02457
993 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 206.357 201.409
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] High confidence 211.071 204.205 1.03362
994 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] Low confidence 201.562 196.729 1.02457
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] High confidence 116.845 120.772 1.03361
995 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 219.656 212.547 1.03345
ubiquitin carboxyl-terminal hydrolase 2 (ec 3.1.2.15) (ubiquitin thiolesterase 2) (ubiquitin-specific processing protease 2) (deubiquitinating enzyme 2) (41 kda ubiquitin-specific protease). [swissprot;acc:o75604] Low confidence 200.373 195.574 1.02454
996 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] High confidence 219.656 212.547 1.03345
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Low confidence 204.965 200.057 1.02453
997 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] High confidence 219.656 212.547 1.03345
rd protein. [swissprot;acc:p18615] Low confidence 204.965 200.057 1.02453
998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] High confidence 225.557 218.271 1.03338
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Low confidence 199.985 195.196 1.02453
999 j domain containing protein 1. [swissprot;acc:q9ukb3] 204.965 200.057
vinculin (metavinculin). [swissprot;acc:p18206] High confidence 215.92 208.95 1.03336
1000 hematopoietic lineage cell specific protein (hematopoietic cell- specific lyn substrate 1) (lckbp1). [swissprot;acc:p14317] Low confidence 199.945 195.159 1.02452
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] High confidence 225.167 217.922 1.03325

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/