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 3608 to 3657 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1804 germ cell-less. [refseq;acc:nm_022471] Subtracted 206.335 203.877 2.458
1805 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Divided 217.008 214.482 1.01178
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Subtracted 206.332 203.874 2.458
1806 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Divided 217.009 214.482 1.01178
hyporthetical protein mgc27169. [refseq;acc:nm_176782] Subtracted 206.332 203.874 2.458
1807 homeobox protein meis1. [swissprot;acc:o00470]
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] Divided 211.102 208.651 1.01175
1808 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Subtracted 206.332 203.874 2.458
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Divided 211.102 208.651 1.01175
1809 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Subtracted 206.332 203.874 2.458
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Divided 211.102 208.651 1.01175
1810 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 223.214 225.827 1.01171
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Subtracted 206.332 203.874 2.458
1811 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Divided 216.854 214.35 1.01168
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Subtracted 206.332 203.874 2.458
1812 cyclin c. [swissprot;acc:p24863] Divided 217.071 214.564 1.01168
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Subtracted 206.332 203.874 2.458
1813 ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] 211.102 208.651 2.451
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Divided 216.854 214.35 1.01168
1814 ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Subtracted 211.102 208.651 2.451
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 122.3 123.727 1.01167
1815 dpy-30-like protein. [swissprot;acc:q9c005] 220.462 217.926 1.01164
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Subtracted 211.102 208.651 2.451
1816 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 187.582 190.028 2.446
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Divided 220.462 217.926 1.01164
1817 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Subtracted 214.722 212.281 2.441
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Divided 220.462 217.926 1.01164
1818 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] Subtracted 212.884 215.323 2.439
neighbor of cox4. [swissprot;acc:o43402] Divided 220.462 217.926 1.01164
1819 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Subtracted 233.828 231.395 2.433
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Divided 220.462 217.926 1.01164
1820 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Subtracted 233.828 231.395 2.433
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 220.462 217.926 1.01164
1821 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Subtracted 201.288 198.86 2.428
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Divided 218.36 215.874 1.01152
1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 240.32 243.085 1.01151
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Subtracted 222.215 224.637 2.422
1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Divided 202.386 200.086 1.0115
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Subtracted 222.215 224.637 2.422
1824 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Divided 214.722 212.281 1.0115
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Subtracted 214.746 212.328 2.418
1825 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 203.759 201.349 2.41
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Divided 202.386 200.086 1.0115
1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 202.393 200.094 1.01149
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Subtracted 223.862 226.271 2.409
1827 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 222.819 225.228
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided 191.39 189.219 1.01147
1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 202.41 200.115
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Subtracted 223.862 226.271 2.409
1829 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] Divided 212.884 215.323 1.01146

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.
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