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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Value Type Rank Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1080 to 1129 of 12912 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
1080 SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 6439.3 7031.73 1.092
1081 SCAMP3 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
1082 SCAMP1 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 6439.35 7031.8
1083 EXOC6B exocyst complex component sec15b. [swissprot;acc:q9y2d4] 6213.51 6785.04 1.09198
1084 CDS2 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 1.09192
1085 SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 6520.28 7119.28 1.09187
1086 PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]
1087 JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] 5732.73 6256.63 1.09139
1088 no value tax interaction protein 1. [refseq;acc:nm_014604]
1089 AGXT 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 1.0912
1090 FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 5651.07 6164.55 1.09086
1091 PABPC3 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 5791.05 6316.61 1.09075
1092 KIN hskin17 protein. [refseq;acc:nm_012311]
1093 CRAT carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]
1094 PABPC4 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 PABPC1 polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]
1096 KIF2B kinesin protein. [refseq;acc:nm_032559] 5356.23 5842.15 1.09072
1097 MAF1 homolog of yeast maf1. [refseq;acc:nm_032272] 6133.83 6690.18 1.0907
1098 SERINC2 tumor differentially expressed protein 2. [refseq;acc:nm_178865]
1099 SERINC3 tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]
1100 SERINC1 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
1101 PHGDH d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1102 FARSB phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 5462.88 5958.12 1.09066
1103 KIF21A ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] 5358.18 5843.73 1.09062
1104 KIF2A kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] 5359.72 5844.97 1.09054
1105 SYT12 synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] 5460.49 5954.62 1.09049
1106 MSRA 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 1.09046
1107 PSAT1 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
1108 PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 4846.16 5283.08 1.09016
1109 RAB3IL1 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 6545.19 7132.89 1.08979
1110 FDXR nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 5947.53 6481.56
1111 RAB3IP rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 6540.61 7127.41 1.08972
1112 PGAM4 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
1113 no value 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 PGAM2 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 MTR 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 5795.13 6314.19 1.08957
1116 DCTN2 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] 5322.16 5798.38 1.08948
1117 SLC25A6 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]
1118 SLC25A4 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235]
1119 SLC25A5 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141]
1120 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 5915.42 6443.77 1.08932
1121 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 4338.49 4725.86 1.08929
1122 IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] 7937.72 8646.38 1.08928
1123 ASL argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 5857.48 6380.4 1.08927
1124 TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] 6288.27 6846.97 1.08885
1125 no value transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 6287.07 6845.28 1.08879
1126 KPNA6 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 5792.08 6305.67 1.08867
1127 YIF1A yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] 5790.65 6303.92 1.08864
1128 KCNAB3 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 6303.94
1129 KCNAB1 voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] 6303.92

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
- Hugo is the HGNC identifier if it exists
- 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/