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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Network Comparison Type Gene Value Type Rank Interaction Map network_comparison description red green Filtered
Results: HTML CSV LaTeX Showing element 1068 to 1117 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
network_comparison
description
red
green
1068 1.09237 exocyst complex component sec15a. [swissprot;acc:q8tag9] 6201.54 6774.35
1069 1.09215 elongation factor 2 (ef-2). [swissprot;acc:p13639] 5494.73 6001.08
1070 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]
1071 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]
1072 1.09214 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 5207.39 5687.2
1073 prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]
1074 uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9]
1075 1.09211 phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 6441.56 7034.86
1076 1.09202 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 6439.63 7032.19
1077 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] 6439.66 7032.22
1078 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 6439.63 7032.19
1079 solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 6439.66 7032.22
1080 1.092 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 6439.3 7031.73
1081 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
1082 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 6439.35 7031.8
1083 1.09198 exocyst complex component sec15b. [swissprot;acc:q9y2d4] 6213.51 6785.04
1084 1.09192 phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] 6437.49 7029.22
1085 1.09187 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 6520.28 7119.28
1086 proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]
1087 1.09139 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] 5732.73 6256.63
1088 tax interaction protein 1. [refseq;acc:nm_014604]
1089 1.0912 serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] 6390.28 6973.08
1090 1.09086 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 5651.07 6164.55
1091 1.09075 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 5791.05 6316.61
1092 hskin17 protein. [refseq;acc:nm_012311]
1093 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]
1094 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]
1095 polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]
1096 1.09072 kinesin protein. [refseq;acc:nm_032559] 5356.23 5842.15
1097 1.0907 homolog of yeast maf1. [refseq;acc:nm_032272] 6133.83 6690.18
1098 tumor differentially expressed protein 2. [refseq;acc:nm_178865]
1099 tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]
1100 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
1101 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1102 1.09066 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 5462.88 5958.12
1103 1.09062 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] 5358.18 5843.73
1104 1.09054 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] 5359.72 5844.97
1105 1.09049 synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] 5460.49 5954.62
1106 1.09046 peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 5489.99 5986.63
1107 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
1108 1.09016 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 4846.16 5283.08
1109 1.08979 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 6545.19 7132.89
1110 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 5947.53 6481.56
1111 1.08972 rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 6540.61 7127.41
1112 1.08968 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
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]
1114 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]
1115 1.08957 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 5795.13 6314.19
1116 1.08948 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] 5322.16 5798.38
1117 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]

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/