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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Interaction Map Gene Rank Network Comparison Type green description Filtered red Value Type network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Interaction Map  : High confidence
Value Type  : Measured
Rank
Network Comparison Type
green
description
Filtered
red
network_comparison
1 Divided 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 364 36400000
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] 1 450.5 5.31521
Subtracted 6410 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 85 6325
33356.5 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 1 41482.5 8126
2 Divided 174 cab2. [refseq;acc:nm_033419] 0 0.00001 17400000
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 450.5 5.31521
Subtracted 6410 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 85 6325
33356.5 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1 41482.5 8126
3 Divided 109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 0.00001 10900000
698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 2597.5 3.71868
Subtracted 19621.3 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 0 23818.1 4196.8
33356.5 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 41482.5 8126
4 Divided 89 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 0.00001 8900000
698.5 hbs1-like. [refseq;acc:nm_006620] 1 2597.5 3.71868
Subtracted 21730 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 18704 3026
33356.5 cytohesin 4. [swissprot;acc:q9uia0] 1 41482.5 8126
5 Divided 89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 0.00001 8900000
339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 1153.5 3.39764
Subtracted 24446.3 histone h4. [swissprot;acc:p02304] 0 21773.1 2673.2
33356.5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1 41482.5 8126
6 Divided 89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 0.00001 8900000
339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 1153.5 3.39764
Subtracted 15605.1 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 13174.7 2430.4
36927.5 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 44490.5 7563
7 Divided 43 sedlin. [swissprot;acc:o14582] 0 0.00001 4300000
339.5 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 1 1153.5 3.39764
Subtracted 15605.1 zinc finger protein 277. [swissprot;acc:q9nrm2] 0 13174.7 2430.4
28492 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 21185 7307
8 Divided 43 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 0.00001 4300000
339.5 db83 protein. [swissprot;acc:p57088] 1 1153.5 3.39764
Subtracted 7500.75 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 5106.93 2393.82
28492 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 21185 7307
9 Divided 1281.5 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 398.5 3.21581
6410 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 85 75.4118
Subtracted 14756 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 12478 2278
28492 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 21185 7307
10 Divided 1281.5 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 398.5 3.21581
6410 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 85 75.4118
Subtracted 6193.07 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 7830.62 1637.55
28492 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 21185 7307
11 Divided 5.56738 serpin b12. [swissprot;acc:q96p63] 0 199.549 35.8425
1281.5 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 398.5 3.21581
Subtracted 7252.02 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 0 5734.28 1517.74
28492 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 21185 7307
12 Divided 5.71669 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 199.249 34.8539
1281.5 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 398.5 3.21581
Subtracted 7099.51 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 0 5629.62 1469.89
40795.8 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 34190.9 6604.9
13 Divided 47 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 1363 29
1281.5 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 398.5 3.21581

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/