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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 8289 in total
Network Comparison Type  : Divided
Value Type  : Measured
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
3204 vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296] High confidence 0.00001 0.00001 1
3205 rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Low confidence 8255.96 8481.07 1.02727
3206 mo25-like protein. [swissprot;acc:q9h9s4] 8185 8408.19
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] High confidence 0.00001 0.00001 1
3207 complement component c8 beta chain precursor. [swissprot;acc:p07358]
high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347] Low confidence 7839.44 8053.26 1.02727
3208 fibrillin 1 precursor. [swissprot;acc:p35555] 8012.62 8230.96 1.02725
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761] High confidence 0.00001 0.00001 1
3209 cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948]
fibrillin 3. [refseq;acc:nm_032447] Low confidence 8012.79 8231.1 1.02725
3210 trabid protein. [swissprot;acc:q9ugi0] High confidence 0.00001 0.00001 1
tyrosine-protein kinase tec (ec 2.7.1.112). [swissprot;acc:p42680] Low confidence 7897.46 8112.69 1.02725
3211 cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] High confidence 0.00001 0.00001 1
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Low confidence 7869.67 8084.1 1.02725
3212 endothelial pas domain protein 1 (epas-1) (member of pas protein 2) (mop2) (hypoxia-inducible factor 2 alpha) (hif-2 alpha) (hif2 alpha) (hif-1 alpha-like factor) (hlf). [swissprot;acc:q99814] 8169.06 8391.69
rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788] High confidence 0.00001 0.00001 1
3213 malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]
tyrosine-protein kinase itk/tsk (ec 2.7.1.112) (t-cell-specific kinase) (tyrosine-protein kinase lyk) (kinase emt). [swissprot;acc:q08881] Low confidence 7897.46 8112.69 1.02725
3214 bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] High confidence 0.00001 0.00001 1
complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Low confidence 7897.46 8112.69 1.02725
3215 hypoxia-inducible factor 1 alpha (hif-1 alpha) (hif1 alpha) (arnt interacting protein) (member of pas protein 1) (mop1). [swissprot;acc:q16665] 8169.25 8391.84
membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [swissprot;acc:o43462] High confidence 0.00001 0.00001 1
3216 dna excision repair protein ercc-1. [swissprot;acc:p07992]
tyrosine-protein kinase txk (ec 2.7.1.112). [swissprot;acc:p42681] Low confidence 7897.46 8112.69 1.02725
3217 sex comb on midleg homolog 1. [refseq;acc:nm_012236] High confidence 0.00001 0.00001 1
tyrosine-protein kinase btk (ec 2.7.1.112) (bruton's tyrosine kinase) (agammaglobulinaemia tyrosine kinase) (atk) (b cell progenitor kinase) (bpk). [swissprot;acc:q06187] Low confidence 7897.46 8112.69 1.02725
3218 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] 7868.33 8082.66 1.02724
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] High confidence 0.00001 0.00001 1
3219 growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Low confidence 7868.29 8082.61 1.02724
protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] High confidence 0.00001 0.00001 1
3220 katanin p60 subunit a 1. [refseq;acc:nm_007044] Low confidence 7787.3 7999.35 1.02723
transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] High confidence 0.00001 0.00001 1
3221 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Low confidence 8049.1 8268.25 1.02723
platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034] High confidence 0.00001 0.00001 1
3222 aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Low confidence 7829.65 8042.67 1.02721
3223 heat shock 70 kda protein 1-hom (hsp70-hom). [swissprot;acc:p34931] 8100.68 8321.06
ras-related protein ral-a. [swissprot;acc:p11233] High confidence 0.00001 0.00001 1
3224 carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] Low confidence 7864.66 8078.58 1.0272
integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] High confidence 0.00001 0.00001 1
3225 carbohydrate (keratan sulfate gal-6) sulfotransferase 1; carbohydrate (chondroitin 6/keratan) sulfotransferase 1. [refseq;acc:nm_003654] Low confidence 7864.66 8078.58 1.0272
heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] High confidence 0.00001 0.00001 1
3226 carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Low confidence 7864.66 8078.58 1.0272
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] High confidence 0.00001 0.00001 1
3227 69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]
heat shock 70 kda protein 6 (heat shock 70 kda protein b'). [swissprot;acc:p17066] Low confidence 8100.51 8320.86 1.0272
3228 ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423] High confidence 0.00001 0.00001 1
ralbp1 associated eps domain containing 2; partner of ral-binding protein 1. [refseq;acc:nm_004726] Low confidence 7864.66 8078.58 1.0272
3229 pro-neuregulin-2 precursor (pro-nrg2) [contains: neuregulin-2 (nrg-2) (neural-and thymus-derived activator for erbb kinases) (ntak) (divergent of neuregulin 1) (don-1)]. [swissprot;acc:o14511]

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/