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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1088 tax interaction protein 1. [refseq;acc:nm_014604] Divided 6256.63 5732.73 1.09139
1089 glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Subtracted 6959.21 6439.79 519.42
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Divided 6973.08 6390.28 1.0912
1090 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Subtracted 6959.21 6439.79 519.42
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Divided 6164.55 5651.07 1.09086
1091 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Subtracted 6029.29 5509.89 519.4
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Divided 6316.61 5791.05 1.09075
1092 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Subtracted 5884.43 5365.14 519.29
hskin17 protein. [refseq;acc:nm_012311] Divided 6316.61 5791.05 1.09075
1093 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Subtracted 5884.32 5365.22 519.1
1094 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 6314.19 5795.13 519.06
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] Divided 6316.61 5791.05 1.09075
1095 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Subtracted 4633.96 4115.39 518.57
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Divided 6316.61 5791.05 1.09075
1096 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Subtracted 6852.61 6334.15 518.46
kinesin protein. [refseq;acc:nm_032559] Divided 5842.15 5356.23 1.09072
1097 60s ribosomal protein l39. [swissprot;acc:p02404] Subtracted 5226.71 4708.61 518.1
homolog of yeast maf1. [refseq;acc:nm_032272] Divided 6690.18 6133.83 1.0907
1098 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted 5226.71 4708.61 518.1
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Divided 6690.18 6133.83 1.0907
1099 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 5226.71 4708.61 518.1
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Divided 6690.18 6133.83 1.0907
1100 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 5226.71 4708.61 518.1
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Divided 6690.18 6133.83 1.0907
1101 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Subtracted 7238.34 6721.25 517.09
1102 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided 5958.12 5462.88 1.09066
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Subtracted 7950.61 7433.73 516.88
1103 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Divided 5843.73 5358.18 1.09062
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Subtracted 7950.61 7433.73 516.88
1104 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Divided 5844.97 5359.72 1.09054
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Subtracted 7950.61 7433.73 516.88
1105 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Divided 5954.62 5460.49 1.09049
1106 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Subtracted 7950.61 7433.73 516.88
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Divided 5986.63 5489.99 1.09046
1107 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Subtracted 7950.61 7433.73 516.88
1108 nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494]
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Divided 5283.08 4846.16 1.09016
1109 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Subtracted 7950.61 7433.73 516.88
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Divided 7132.89 6545.19 1.08979
1110 mstp028 protein. [refseq;acc:nm_031954] Subtracted 6355.06 5838.87 516.19
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Divided 6481.56 5947.53 1.08979
1111 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Subtracted 5909.47 5393.37 516.1
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Divided 7127.41 6540.61 1.08972
1112 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 6440.58 5910.54 1.08968
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Subtracted 6355.56 5840.01 515.55
1113 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] Divided 6440.58 5910.54 1.08968

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/