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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7412 to 7461 of 19268 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1181 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Divided High confidence 218.186 212.672 1.02593
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Subtracted Low confidence 202.873 198.325 4.548
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] Divided 201.302 196.744 1.02317
1182 ecotropic virus integration 1 site protein. [swissprot;acc:q03112] Subtracted 203.266 198.72 4.546
neurocalcin delta. [swissprot;acc:p29554] Divided High confidence 225.104 230.931 1.02589
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Low confidence 206.598 201.924 1.02315
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Subtracted High confidence 218.269 212.918 5.351
1183 diaphanous protein homolog 3 (diaphanous-related formin 3) (drf3) (fragment). [swissprot;acc:q9nsv4] Low confidence 200.258 195.713 4.545
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] High confidence 219.354 224.7 5.346
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Divided 225.103 230.928 1.02588
tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] Low confidence 203.427 198.825 1.02315
1184 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] High confidence 216.729 222.334 1.02586
iroquois-class homeodomain protein irx-3 (iroquois homeobox protein 3) (fragment). [swissprot;acc:p78415] Low confidence 195.226 190.812 1.02313
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Subtracted High confidence 219.354 224.7 5.346
snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966] Low confidence 202.718 198.176 4.542
1185 iroquois-class homeodomain protein irx-5 (iroquois homeobox protein 5) (irx-2a). [swissprot;acc:p78411] Divided 195.226 190.812 1.02313
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Subtracted High confidence 219.354 224.7 5.346
microfibrillar-associated protein 1. [swissprot;acc:p55081] Low confidence 202.718 198.176 4.542
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] Divided High confidence 225.094 230.913 1.02585
1186 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 212.904 1.02582
iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1] Low confidence 195.226 190.812 1.02313
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Subtracted 203.529 198.989 4.54
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] High confidence 219.354 224.7 5.346
1187 iroquois-class homeodomain protein irx-1 (iroquois homeobox protein 1) (fragment). [swissprot;acc:p78414] Divided Low confidence 195.226 190.812 1.02313
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Subtracted High confidence 219.354 224.7 5.346
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Low confidence 201.092 196.553 4.539
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Divided High confidence 218.402 212.904 1.02582
1188 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Subtracted 219.354 224.7 5.346
histone h1.5 (histone h1a). [swissprot;acc:p16401] Low confidence 198.047 193.51 4.537
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 202.963 198.378 1.02311
1189 7-dehydrocholesterol reductase (ec 1.3.1.21) (7-dhc reductase) (sterol delta-7-reductase) (putative sterol reductase sr-2). [swissprot;acc:q9ubm7] Subtracted 203.51 198.973 4.537
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Divided High confidence 209.649 204.406 1.02565
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Low confidence 195.344 190.932 1.02311
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Subtracted High confidence 219.354 224.7 5.346
1190 bleomycin hydrolase (ec 3.4.22.40) (blm hydrolase) (bmh) (bh). [swissprot;acc:q13867] Divided Low confidence 202.963 198.378 1.02311
histone h1.4 (histone h1b). [swissprot;acc:p10412] Subtracted 198.05 193.513 4.537
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] High confidence 219.354 224.7 5.346
ubiquitin. [swissprot;acc:p02248] Divided 209.6 204.372 1.02558
1191 histone h1.1. [swissprot;acc:q02539] Subtracted Low confidence 198.054 193.517 4.537
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] High confidence 219.354 224.7 5.346
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Divided 220.742 215.237 1.02558
zinc finger protein gli3. [swissprot;acc:p10071] Low confidence 203.052 198.466 1.02311
1192 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 199.02 194.529 1.02309
putative protein-tyrosine phosphatase tpte (ec 3.1.3.48). [swissprot;acc:p56180] Subtracted 203.336 198.8 4.536
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] High confidence 219.354 224.7 5.346
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Divided 220.742 215.237 1.02558
1193 lbp-9. [refseq;acc:nm_014553]
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Subtracted 219.354 224.7 5.346
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Low confidence 203.499 198.964 4.535

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/