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 3051 to 3100 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1526 cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] High confidence 219.306 223.179 1.01766
krueppel-like factor 13 (transcription factor bteb3) (basic transcription element binding protein 3) (bte-binding protein 3) (rantes factor of late activated t lymphocytes-1) (rflat-1) (transcription factor nslp1) (novel sp1-like zinc finger transcription factor 1). [swissprot;acc:q9y2y9] Low confidence 204.198 199.941 1.02129
1527 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] High confidence 219.306 223.179 1.01766
transcription factor sp2. [swissprot;acc:q02086] Low confidence 204.196 199.94 1.02129
1528 cgi-121 protein; prpk (p53-related protein kinase)-binding protein. [refseq;acc:nm_016058] 192.391 188.381
hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] High confidence 217.785 214.021 1.01759
1529 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 216.762 213.031 1.01751
transcription factor bteb4 (basic transcription element binding- protein 4) (bte-binding protein 4) (krueppel-like factor 16) (novel sp1-like zinc finger transcription factor 2) (transcription factor nslp2). [swissprot;acc:q9bxk1] Low confidence 204.197 199.94 1.02129
1530 af-6 protein. [swissprot;acc:p55196] High confidence 218.733 214.98 1.01746
developmentally regulated gtp-binding protein 2 (drg 2). [swissprot;acc:p55039] Low confidence 202.231 198.015 1.02129
1531 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 195.485 191.412 1.02128
cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] High confidence 217.025 213.304 1.01744
1532 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Low confidence 203.549 199.307 1.02128
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] High confidence 228.419 232.376 1.01732
1533 cytochrome c. [swissprot;acc:p00001]
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Low confidence 203.346 199.108 1.02128
1534 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] High confidence 228.419 232.376 1.01732
mo25-like protein. [swissprot;acc:q9h9s4] Low confidence 200.515 196.337 1.02128
1535 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] High confidence 228.419 232.376 1.01732
serine/threonine-protein kinase chk2 (ec 2.7.1.-) (cds1). [swissprot;acc:o96017] Low confidence 200.266 196.095 1.02127
1536 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 198.934 194.79
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] High confidence 228.419 232.376 1.01732
1537 dead-box protein 3, y-chromosomal. [swissprot;acc:o15523] Low confidence 200.879 196.696 1.02127
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] High confidence 228.419 232.376 1.01732
1538 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
mo25 protein (cgi-66). [swissprot;acc:q9y376] Low confidence 200.517 196.343 1.02126
1539 dead-box protein 3 (helicase-like protein 2) (hlp2) (dead-box, x isoform). [swissprot;acc:o00571] 200.878 196.696
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] High confidence 228.419 232.376 1.01732
1540 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 240.077 236.015 1.01721
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] Low confidence 201.26 197.072 1.02125
1541 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 203.321 199.093 1.02124
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] High confidence 222.672 218.92 1.01714
1542 trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] 213.546 209.965 1.01706
vav-2 protein. [swissprot;acc:p52735] Low confidence 200.389 196.224 1.02123
1543 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] High confidence 213.546 209.965 1.01706
homeobox protein hox-b6 (hox-2b) (hox-2.2) (hu-2). [swissprot;acc:p17509] Low confidence 203.129 198.906 1.02123
1544 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] High confidence 219.762 216.081 1.01704
park2 co-regulated; parkin co-regulated gene protein. [refseq;acc:nm_152410] Low confidence 203.124 198.907 1.0212
1545 orphan nuclear receptor tr2. [swissprot;acc:p13056] High confidence 219.76 216.083 1.01702
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Low confidence 199.511 195.372 1.02119
1546 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] High confidence 217.769 221.474 1.01701
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Low confidence 201.261 197.087 1.02118
1547 myb-related protein b (b-myb). [swissprot;acc:p10244] High confidence 222.541 218.823 1.01699
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Low confidence 202.348 198.152 1.02118
1548 myb-related protein a (a-myb). [swissprot;acc:p10243] High confidence 222.512 218.802 1.01696
ubiquitin conjugation factor e4 b (ubiquitin-fusion degradation protein 2) (homozygously deleted in neuroblastoma-1). [swissprot;acc:o95155] Low confidence 202.493 198.294 1.02118
1549 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 205.847 201.577
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] High confidence 225.159 221.424 1.01687
1550 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]
ras-related protein rab-6c (rab6-like protein wth3). [swissprot;acc:q9h0n0] Low confidence 200.571 196.413 1.02117

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/