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 description Network Comparison Type Filtered Value Type green network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Interaction Map  : High confidence
Value Type  : Measured
Rank
description
Network Comparison Type
Filtered
green
network_comparison
red
1 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 0 6410 6325 85
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 33356.5 8126 41482.5
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 0 0.00001 36400000 364
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 2394.5 5.31521 450.5
2 cab2. [refseq;acc:nm_033419] 0 174 17400000 0.00001
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Subtracted 1 33356.5 8126 41482.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 6410 6325 85
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided 1 2394.5 5.31521 450.5
3 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Subtracted 33356.5 8126 41482.5
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided 698.5 3.71868 2597.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 0 19621.3 4196.8 23818.1
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided 109 10900000 0.00001
4 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 1 33356.5 8126 41482.5
hbs1-like. [refseq;acc:nm_006620] Divided 698.5 3.71868 2597.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 89 8900000 0.00001
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 21730 3026 18704
5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1 33356.5 8126 41482.5
histone h4. [swissprot;acc:p02304] 0 24446.3 2673.2 21773.1
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 89 8900000 0.00001
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 339.5 3.39764 1153.5
6 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 89 8900000 0.00001
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 339.5 3.39764 1153.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 36927.5 7563 44490.5
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 15605.1 2430.4 13174.7
7 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 28492 7307 21185
sedlin. [swissprot;acc:o14582] Divided 0 43 4300000 0.00001
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] 1 339.5 3.39764 1153.5
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted 0 15605.1 2430.4 13174.7
8 db83 protein. [swissprot;acc:p57088] Divided 1 339.5 3.39764 1153.5
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted 0 7500.75 2393.82 5106.93
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 28492 7307 21185
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided 0 43 4300000 0.00001
9 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted 14756 2278 12478
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided 6410 75.4118 85
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Subtracted 1 28492 7307 21185
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided 1281.5 3.21581 398.5
10 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 6410 75.4118 85
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 6193.07 1637.55 7830.62
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 28492 7307 21185
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 1281.5 3.21581 398.5
11 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 0 7252.02 1517.74 5734.28
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided 1 1281.5 3.21581 398.5
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted 28492 7307 21185
serpin b12. [swissprot;acc:q96p63] Divided 0 5.56738 35.8425 199.549
12 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 7099.51 1469.89 5629.62
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided 1 1281.5 3.21581 398.5
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 5.71669 34.8539 199.249
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 1 40795.8 6604.9 34190.9
13 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Divided 0 47 29 1363
Subtracted 1316

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/