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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2180 to 2229 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1090 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Divided 5651.07 6164.55 1.09086
1091 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Subtracted 5509.89 6029.29 519.4
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Divided 5791.05 6316.61 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 5365.14 5884.43 519.29
hskin17 protein. [refseq;acc:nm_012311] Divided 5791.05 6316.61 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 5365.22 5884.32 519.1
1094 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 5795.13 6314.19 519.06
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 5791.05 6316.61 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 4115.39 4633.96 518.57
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Divided 5791.05 6316.61 1.09075
1096 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Subtracted 6334.15 6852.61 518.46
kinesin protein. [refseq;acc:nm_032559] Divided 5356.23 5842.15 1.09072
1097 60s ribosomal protein l39. [swissprot;acc:p02404] Subtracted 4708.61 5226.71 518.1
homolog of yeast maf1. [refseq;acc:nm_032272] Divided 6133.83 6690.18 1.0907
1098 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted 4708.61 5226.71 518.1
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Divided 6133.83 6690.18 1.0907
1099 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 4708.61 5226.71 518.1
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Divided 6133.83 6690.18 1.0907
1100 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 4708.61 5226.71 518.1
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Divided 6133.83 6690.18 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 6721.25 7238.34 517.09
1102 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided 5462.88 5958.12 1.09066
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Subtracted 7433.73 7950.61 516.88
1103 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Divided 5358.18 5843.73 1.09062
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Subtracted 7433.73 7950.61 516.88
1104 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Divided 5359.72 5844.97 1.09054
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Subtracted 7433.73 7950.61 516.88
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 5460.49 5954.62 1.09049
1106 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Subtracted 7433.73 7950.61 516.88
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Divided 5489.99 5986.63 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 7433.73 7950.61 516.88
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 4846.16 5283.08 1.09016
1109 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Subtracted 7433.73 7950.61 516.88
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Divided 6545.19 7132.89 1.08979
1110 mstp028 protein. [refseq;acc:nm_031954] Subtracted 5838.87 6355.06 516.19
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Divided 5947.53 6481.56 1.08979
1111 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Subtracted 5393.37 5909.47 516.1
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Divided 6540.61 7127.41 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] 5910.54 6440.58 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 5840.01 6355.56 515.55
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 5910.54 6440.58 1.08968
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Subtracted 5950.27 6465.72 515.45
1114 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 6021.21 6536.45 515.24
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] Divided 5910.54 6440.58 1.08968
1115 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 5795.13 6314.19 1.08957

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/