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 4480 to 4529 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1120 myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Rooted 55.1167 57.8361 1.04934
1121 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Squared 24431.4 27918.1 1.14271
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Measured 4338.49 4725.86 1.08929
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Rooted 56.3761 59.1441 1.0491
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Ranked 218.529 212.676 1.02752
1122 casein kinase i alpha s-like. [refseq;acc:nm_145203] Rooted 57.0994 59.9007 1.04906
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Measured 7937.72 8646.38 1.08928
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Squared 25154 28740.5 1.14258
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Ranked 218.527 212.676 1.02751
1123 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] Measured 5857.48 6380.4 1.08927
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Rooted 57.0994 59.9007 1.04906
hskin17 protein. [refseq;acc:nm_012311] Squared 25154 28740.5 1.14258
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Ranked 169.031 164.507 1.0275
1124 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Squared 25154 28740.5 1.14258
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Ranked 207.553 213.256 1.02748
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Rooted 63.5285 66.6395 1.04897
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Measured 6288.27 6846.97 1.08885
1125 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Ranked 204.404 210.022 1.02748
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Rooted 63.5285 66.6395 1.04897
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Squared 25154 28740.5 1.14258
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Measured 6287.07 6845.28 1.08879
1126 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Ranked 218.487 212.656 1.02742
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Measured 5792.08 6305.67 1.08867
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Rooted 63.5285 66.6395 1.04897
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Squared 25154 28740.5 1.14258
1127 60s ribosomal protein l39. [swissprot;acc:p02404] 18854.4 21540.4 1.14246
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Rooted 59.7501 62.6744 1.04894
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Ranked 239.219 232.837 1.02741
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Measured 5790.65 6303.92 1.08864
1128 60s ribosomal protein l18a. [swissprot;acc:q02543] Squared 18854.4 21540.4 1.14246
60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Rooted 69.8977 73.3177 1.04893
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Ranked 221.286 215.399 1.02733
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Measured 5790.65 6303.94 1.08864
1129 40s ribosomal protein s19. [swissprot;acc:p39019] Squared 18854.4 21540.4 1.14246
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Ranked 221.285 215.401 1.02732
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Rooted 61.8294 64.8484 1.04883
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Measured 5790.65 6303.92 1.08864
1130 60s ribosomal protein l31. [swissprot;acc:p12947] Squared 18854.4 21540.4 1.14246
ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] Rooted 61.8294 64.8484 1.04883
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Ranked 221.285 215.4 1.02732
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Measured 5790.65 6303.92 1.08864
1131 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Squared 20739 23691.8 1.14238
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Rooted 53.3231 50.8416 1.04881
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] Ranked 218.484 212.675 1.02731
1132 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Measured 5790.65 6303.92 1.08864
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Ranked 218.484 212.675 1.02731
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Squared 20709.5 23652.8 1.14212
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Rooted 64.7804 67.9395 1.04877
1133 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Squared 29990.9 34251.1 1.14205

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/