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