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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6186 to 6235 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
3093 no value ptd016 protein. [refseq;acc:nm_016125] Subtracted 0 0 0
3094 UBE2S ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3095 C10orf137 erythroid differentiation-related factor 1. [refseq;acc:nm_015608] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3096 NPM3 nucleoplasmin 3. [swissprot;acc:o75607] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3097 SEC23IP sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3098 EZH2 enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3099 CAV1 caveolin-1. [swissprot;acc:q03135] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3100 no value presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3101 gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3102 C19orf56 protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3103 LIG1 dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3104 SNORD23 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3105 TGFB1 transforming growth factor beta 1 precursor (tgf-beta 1). [swissprot;acc:p01137] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3106 PTOV1 prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3107 LYL1 lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3108 SNX16 sorting nexin 16. [swissprot;acc:p57768] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3109 WISP1 wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3110 RAB2A ras-related protein rab-2a. [swissprot;acc:p08886] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3111 STK3 serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3112 RAB11A ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3113 NUTF2 nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3114 TSC22D1 regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3115 STK24 serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [swissprot;acc:q9y6e0] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3116 CAB39L mo25-like protein. [swissprot;acc:q9h9s4] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3117 FNDC3A ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] Divided 0.00001 0.00001 1
Subtracted 0 0 0
3118 SMS spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788] Divided 0.00001 0.00001 1

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
- Hugo is the HGNC identifier if it exists
- 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/