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.


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Gene Value Type Rank network_comparison green description Filtered Network Comparison Type Interaction Map red
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Measured
Rank
network_comparison
green
description
Filtered
Network Comparison Type
Interaction Map
red
1 4.4149 543.5 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 1 Divided Low confidence 2399.5
5.31521 2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 450.5
6325 6410 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 Subtracted 85
Low confidence
8126 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 High confidence 41482.5
8870.5 32028.5 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 40899
36400000 0.00001 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 Divided High confidence 364
Low confidence
2 4.4149 543.5 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 1 2399.5
5.31521 2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 450.5
4196.8 19621.3 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 0 Subtracted Low confidence 23818.1
6325 6410 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 85
7307 28492 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 Low confidence 21185
8126 33356.5 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 41482.5
8900000 89 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 Divided Low confidence 0.00001
17400000 174 cab2. [refseq;acc:nm_033419] High confidence
3 3.71868 698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 2597.5
4.4149 543.5 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 2399.5
2393.82 7500.75 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 Subtracted 5106.93
4196.8 19621.3 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 23818.1
7307 28492 mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 Low confidence 21185
8126 33356.5 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 41482.5
8900000 89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 Divided Low confidence 0.00001
10900000 109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence
4 3.71868 698.5 hbs1-like. [refseq;acc:nm_006620] 1 2597.5
4.4149 543.5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 2399.5
2274 4356 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 0 Subtracted 2082
3026 21730 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 18704
7035.1 43509.4 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 1 Low confidence 36474.3
8126 33356.5 cytohesin 4. [swissprot;acc:q9uia0] High confidence 41482.5
8900000 89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 Divided Low confidence 0.00001
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
5 2.86965 2113.5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 1 Low confidence 736.5
3.39764 339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 1153.5
2254.84 2740.13 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 Subtracted Low confidence 485.286
2673.2 24446.3 histone h4. [swissprot;acc:p02304] High confidence 21773.1
7034 43503.3 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 1 Low confidence 36469.3
8126 33356.5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] High confidence 41482.5
1751660 17.5166 jumonji protein. [swissprot;acc:q92833] 0 Divided Low confidence 0.00001
8900000 89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence
6 2.86965 2113.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 1 Low confidence 736.5
3.39764 339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 1153.5
1244.48 8836.85 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 Subtracted Low confidence 7592.37
2430.4 15605.1 High confidence 13174.7
7008.5 43368.8 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 Low confidence 36360.3
7563 36927.5 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 44490.5
1300000 0.00001 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0 Divided Low confidence 13
8900000 89 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 0.00001
7 2.86965 2113.5 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 1 Low confidence 736.5
3.39764 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] High confidence 1153.5

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/