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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank description Gene Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 330 to 379 of 515 in total
Network Comparison Type  : Subtracted
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0
Rank
description
Hugo
3085 udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] UGT2B10
3086 udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] no value
3087 fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972] ALDOC
3088 14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655] YWHAE
3089 camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] PRKAR1A
3090 enhancer of zeste homolog 1 (enx-2). [swissprot;acc:q92800] EZH1
3091 transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [swissprot;acc:q9uh92] MLX
3092 developmentally regulated gtp-binding protein 2 (drg 2). [swissprot;acc:p55039] DRG2
3093 ptd016 protein. [refseq;acc:nm_016125] no value
3094 ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] UBE2S
3095 erythroid differentiation-related factor 1. [refseq;acc:nm_015608] C10orf137
3096 nucleoplasmin 3. [swissprot;acc:o75607] NPM3
3097 sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190] SEC23IP
3098 enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910] EZH2
3099 caveolin-1. [swissprot;acc:q03135] CAV1
3100 presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] no value
3101 gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284]
3102 protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] C19orf56
3103 dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] LIG1
3104 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] SNORD23
3105 transforming growth factor beta 1 precursor (tgf-beta 1). [swissprot;acc:p01137] TGFB1
3106 prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432] PTOV1
3107 lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980] LYL1
3108 sorting nexin 16. [swissprot;acc:p57768] SNX16
3109 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] WISP1
3110 ras-related protein rab-2a. [swissprot;acc:p08886] RAB2A
3111 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] STK3
3112 ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410] RAB11A
3113 nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] NUTF2
3114 regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [swissprot;acc:q15714] TSC22D1
3115 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] STK24
3116 mo25-like protein. [swissprot;acc:q9h9s4] CAB39L
3117 ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] FNDC3A
3118 spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788] SMS
3119 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] no value
3120 sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089] SCML2
3121 glycine receptor alpha-2 chain precursor. [swissprot;acc:p23416] GLRA2
3122 ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [swissprot;acc:p11908] PRPS2
3123 vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0] VAPA
3124 sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3] SAMHD1
3125 gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488] POFUT1
3126 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147] PLCB4
3127 protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437] SEC23B
3128 bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] BMP7
3129 cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048] CSTF1
3130 prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4] PFDN4
3131 protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8] C20orf24
3132 r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491] R3HDML
3133 ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366] IFT52
3134 rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696] RABGGTA

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/