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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4908 to 4957 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2454 succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Subtracted 6237.83 6400.74 162.91
2455 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 6200.39 6362.25 161.86
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Divided 5978.83 6166.89 1.03145
2456 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 3629.21 3467.48 161.73
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Divided 5978.83 6166.89 1.03145
2457 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Subtracted 3624.59 3463.37 161.22
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Divided 4998.72 5155.87 1.03144
2458 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 4751.74 4900.37 1.03128
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Subtracted 4730.66 4891.26 160.6
2459 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 3843.06 3682.72 160.34
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Divided 4751.74 4900.37 1.03128
2460 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Subtracted 3976.48 3816.38 160.1
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Divided 4751.74 4900.37 1.03128
2461 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Subtracted 3633.74 3473.68 160.06
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Divided 5114.15 5272.92 1.03105
2462 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] Subtracted 5996.06 6155.81 159.75
2463 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Divided 5114.15 5272.92 1.03105
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] Subtracted 5996.06 6155.81 159.75
2464 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] Divided 6291.2 6486.07 1.03098
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Subtracted 3977.7 3818.01 159.69
2465 germ cell-less. [refseq;acc:nm_022471] Divided 7764.92 8003.67 1.03075
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Subtracted 3977.76 3818.09 159.67
2466 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 3979.06 3819.84 159.22
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Divided 7765.3 8004 1.03074
2467 pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 3612.45 3453.39 159.06
2468 hyporthetical protein mgc27169. [refseq;acc:nm_176782] Divided 7765.3 8004 1.03074
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Subtracted 5114.15 5272.92 158.77
2469 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
homeobox protein meis1. [swissprot;acc:o00470] Divided 7765.3 8004 1.03074
2470 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Subtracted 5114.15 5272.92 158.77
2471 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Divided 7765.3 8004 1.03074
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Subtracted 6256.49 6415.21 158.72
2472 integral membrane protein cii-3b. [sptrembl;acc:o75609] 6256.42 6415.04 158.62
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Divided 7765.3 8004 1.03074
2473 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Subtracted 6202.78 6360.79 158.01
2474 dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 3619.07 3461.21 157.86
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Divided 7765.3 8004 1.03074
2475 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 4998.72 5155.87 157.15
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Divided 3573.66 3682.14 1.03036
2476 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Subtracted 6203.05 6360.18 157.13
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Divided 3569.07 3676.7 1.03016
2477 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Subtracted 6204.25 6360.69 156.44
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Divided 3568.84 3676.43 1.03015
2478 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Subtracted 6203.92 6360.25 156.33
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 3568.96 3676.57 1.03015
2479 eh-domain containing protein 3. [swissprot;acc:q9nzn3] Subtracted 6203.94 6360.25 156.31

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/