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 Value Type Rank Network Comparison Type Filtered description network_comparison green Interaction Map red
Results: HTML CSV LaTeX Showing element 1 to 50 of 66312 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
network_comparison
green
Interaction Map
red
1 Divided lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 4.4149 543.5 Low confidence 2399.5
rad50-interacting protein 1. [refseq;acc:nm_021930] 5.31521 2394.5 High confidence 450.5
Subtracted carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 8870.5 32028.5 Low confidence 40899
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] 8126 33356.5 High confidence 41482.5
2 Divided cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 4.4149 543.5 Low confidence 2399.5
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 5.31521 2394.5 High confidence 450.5
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 7307 28492 Low confidence 21185
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 8126 33356.5 High confidence 41482.5
3 Divided cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 4.4149 543.5 Low confidence 2399.5
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 698.5 High confidence 2597.5
Subtracted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 8126 33356.5 41482.5
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 7307 28492 Low confidence 21185
4 Divided hbs1-like. [refseq;acc:nm_006620] 3.71868 698.5 High confidence 2597.5
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 4.4149 543.5 Low confidence 2399.5
Subtracted bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 7035.1 43509.4 36474.3
cytohesin 4. [swissprot;acc:q9uia0] 8126 33356.5 High confidence 41482.5
5 Divided junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 3.39764 339.5 1153.5
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2.86965 2113.5 Low confidence 736.5
Subtracted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 8126 33356.5 High confidence 41482.5
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 7034 43503.3 Low confidence 36469.3
6 Divided junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 3.39764 339.5 High confidence 1153.5
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2.86965 2113.5 Low confidence 736.5
Subtracted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 7008.5 43368.8 36360.3
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 7563 36927.5 High confidence 44490.5
7 Divided oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 2.86965 2113.5 Low confidence 736.5
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] 3.39764 339.5 High confidence 1153.5
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 7307 28492 21185
vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682] 7008.5 43368.8 Low confidence 36360.3
8 Divided db83 protein. [swissprot;acc:p57088] 3.39764 339.5 High confidence 1153.5
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 1.54317 5058.5 Low confidence 3278
Subtracted deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 6246.7 39358.1 33111.4
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 7307 28492 High confidence 21185
9 Divided n33 protein. [swissprot;acc:q13454] 1.54317 5058.5 Low confidence 3278
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 3.21581 1281.5 High confidence 398.5
Subtracted pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 7307 28492 21185
sperm associated antigen 7. [refseq;acc:nm_004890] 4037.2 19280.8 Low confidence 23318
10 Divided implantation-associated protein. [refseq;acc:nm_032121] 1.54317 5058.5 3278
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 3.21581 1281.5 High confidence 398.5
Subtracted pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 7307 28492 21185
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 2232.7 17265.4 Low confidence 19498.1
11 Divided dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 3.21581 1281.5 High confidence 398.5
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1.53861 2950.5 Low confidence 1917.64
Subtracted mitochondrial solute carrier protein. [refseq;acc:nm_145305] 7307 28492 High confidence 21185
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 2112.16 9368.87 Low confidence 7256.71
12 Divided cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 3.21581 1281.5 High confidence 398.5
gbp protein isoform a. [refseq;acc:nm_017870] 1.5371 2954.24 Low confidence 1921.96
Subtracted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 2108.6 17572.7 15464.1
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 6604.9 40795.8 High confidence 34190.9
13 Divided cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 3.21581 1281.5 398.5
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] 1.5351 2959.19 Low confidence 1927.68

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/