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 Network Comparison Type description Value Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 1 to 50 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
Network Comparison Type
description
Filtered
red
network_comparison
green
1 Divided mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 364 36400000 0.00001
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 450.5 5.31521 2394.5
Subtracted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 85 6325 6410
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 33356.5
2 Divided cab2. [refseq;acc:nm_033419] 0 0.00001 17400000 174
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 450.5 5.31521 2394.5
Subtracted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 41482.5 8126 33356.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 85 6325 6410
3 Divided homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 2597.5 3.71868 698.5
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 0.00001 10900000 109
Subtracted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 41482.5 8126 33356.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 0 23818.1 4196.8 19621.3
4 Divided hbs1-like. [refseq;acc:nm_006620] 1 2597.5 3.71868 698.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 0.00001 8900000 89
Subtracted cytohesin 4. [swissprot;acc:q9uia0] 1 41482.5 8126 33356.5
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 18704 3026 21730
5 Divided homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 8900000 89
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 1153.5 3.39764 339.5
Subtracted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 8126 33356.5
histone h4. [swissprot;acc:p02304] 0 21773.1 2673.2 24446.3
6 Divided homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 8900000 89
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 1153.5 3.39764 339.5
Subtracted putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 7563 36927.5
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 13174.7 2430.4 15605.1
7 Divided sedlin. [swissprot;acc:o14582] 0.00001 4300000 43
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 339.5
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 21185 7307 28492
zinc finger protein 277. [swissprot;acc:q9nrm2] 0 13174.7 2430.4 15605.1
8 Divided db83 protein. [swissprot;acc:p57088] 1 1153.5 3.39764 339.5
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 0.00001 4300000 43
Subtracted nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 5106.93 2393.82 7500.75
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 21185 7307 28492
9 Divided ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 85 75.4118 6410
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 398.5 3.21581 1281.5
Subtracted ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 0 12478 2278 14756
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 21185 7307 28492
10 Divided lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 85 75.4118 6410
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1 398.5 3.21581 1281.5
Subtracted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 7830.62 1637.55 6193.07
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 21185 7307 28492
11 Divided dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 398.5 3.21581 1281.5
serpin b12. [swissprot;acc:q96p63] 0 199.549 35.8425 5.56738
Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 5734.28 1517.74 7252.02
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 21185 7307 28492
12 Divided cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 398.5 3.21581 1281.5
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 199.249 34.8539 5.71669
Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 5629.62 1469.89 7099.51
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 34190.9 6604.9 40795.8
13 Divided adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 1363 29 47
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 398.5 3.21581 1281.5

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/