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 Interaction Map Gene Rank Network Comparison Type description Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
Network Comparison Type
description
Filtered
green
red
network_comparison
1 Divided mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 0.00001 364 36400000
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 2394.5 450.5 5.31521
Subtracted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 6410 85 6325
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 41482.5 8126
2 Divided cab2. [refseq;acc:nm_033419] 0 174 0.00001 17400000
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 2394.5 450.5 5.31521
Subtracted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 33356.5 41482.5 8126
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 6410 85 6325
3 Divided homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 698.5 2597.5 3.71868
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 109 0.00001 10900000
Subtracted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 33356.5 41482.5 8126
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 0 19621.3 23818.1 4196.8
4 Divided hbs1-like. [refseq;acc:nm_006620] 1 698.5 2597.5 3.71868
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 89 0.00001 8900000
Subtracted cytohesin 4. [swissprot;acc:q9uia0] 1 33356.5 41482.5 8126
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 21730 18704 3026
5 Divided homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 89 0.00001 8900000
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 339.5 1153.5 3.39764
Subtracted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 33356.5 41482.5 8126
histone h4. [swissprot;acc:p02304] 0 24446.3 21773.1 2673.2
6 Divided homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 89 0.00001 8900000
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 339.5 1153.5 3.39764
Subtracted putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 36927.5 44490.5 7563
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 15605.1 13174.7 2430.4
7 Divided sedlin. [swissprot;acc:o14582] 43 0.00001 4300000
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 1153.5 3.39764
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 21185 7307
zinc finger protein 277. [swissprot;acc:q9nrm2] 0 15605.1 13174.7 2430.4
8 Divided db83 protein. [swissprot;acc:p57088] 1 339.5 1153.5 3.39764
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 43 0.00001 4300000
Subtracted nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 7500.75 5106.93 2393.82
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 28492 21185 7307
9 Divided ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 6410 85 75.4118
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 1281.5 398.5 3.21581
Subtracted ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 0 14756 12478 2278
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 28492 21185 7307
10 Divided lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 6410 85 75.4118
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1 1281.5 398.5 3.21581
Subtracted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 6193.07 7830.62 1637.55
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 28492 21185 7307
11 Divided dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1281.5 398.5 3.21581
serpin b12. [swissprot;acc:q96p63] 0 5.56738 199.549 35.8425
Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 7252.02 5734.28 1517.74
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 28492 21185 7307
12 Divided cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1281.5 398.5 3.21581
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 5.71669 199.249 34.8539
Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 7099.51 5629.62 1469.89
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 40795.8 34190.9 6604.9
13 Divided adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 47 1363 29
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 1281.5 398.5 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/