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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Gene Rank Value Type green description Network Comparison Type Interaction Map red network_comparison Filtered
Results: HTML CSV LaTeX Showing element 1 to 50 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
green
description
Network Comparison Type
Interaction Map
red
network_comparison
1 543.5 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided Low confidence 2399.5 4.4149
2394.5 rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 450.5 5.31521
32028.5 carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Subtracted Low confidence 40899 8870.5
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] High confidence 41482.5 8126
2 543.5 cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Divided Low confidence 2399.5 4.4149
2394.5 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 450.5 5.31521
28492 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted Low confidence 21185 7307
33356.5 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 41482.5 8126
3 543.5 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Divided Low confidence 2399.5 4.4149
698.5 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 2597.5 3.71868
28492 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted Low confidence 21185 7307
33356.5 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 41482.5 8126
4 543.5 lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Divided Low confidence 2399.5 4.4149
698.5 hbs1-like. [refseq;acc:nm_006620] High confidence 2597.5 3.71868
33356.5 cytohesin 4. [swissprot;acc:q9uia0] Subtracted 41482.5 8126
43509.4 bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Low confidence 36474.3 7035.1
5 339.5 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Divided High confidence 1153.5 3.39764
2113.5 oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 736.5 2.86965
33356.5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted High confidence 41482.5 8126
43503.3 vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 36469.3 7034
6 339.5 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Divided High confidence 1153.5 3.39764
2113.5 oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 736.5 2.86965
36927.5 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted High confidence 44490.5 7563
43368.8 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 36360.3 7008.5
7 339.5 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] Divided High confidence 1153.5 3.39764
2113.5 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 736.5 2.86965
28492 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted High confidence 21185 7307
43368.8 vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] Low confidence 36360.3 7008.5
8 339.5 db83 protein. [swissprot;acc:p57088] Divided High confidence 1153.5 3.39764
5058.5 phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 3278 1.54317
28492 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Subtracted High confidence 21185 7307
39358.1 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Low confidence 33111.4 6246.7
9 1281.5 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided High confidence 398.5 3.21581
5058.5 n33 protein. [swissprot;acc:q13454] Low confidence 3278 1.54317
19280.8 sperm associated antigen 7. [refseq;acc:nm_004890] Subtracted 23318 4037.2
28492 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 21185 7307
10 1281.5 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 398.5 3.21581
5058.5 implantation-associated protein. [refseq;acc:nm_032121] Low confidence 3278 1.54317
17265.4 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 19498.1 2232.7
28492 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 21185 7307
11 1281.5 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided 398.5 3.21581
2950.5 thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Low confidence 1917.64 1.53861
9368.87 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Subtracted 7256.71 2112.16
28492 mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 21185 7307
12 1281.5 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided 398.5 3.21581
2954.24 gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 1921.96 1.5371
17572.7 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 15464.1 2108.6
40795.8 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 34190.9 6604.9
13 1281.5 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided 398.5 3.21581
2959.19 jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Low confidence 1927.68 1.5351

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/