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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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 Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 308 to 357 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
3063 mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92] MRPS30
3064 complement component c7 precursor. [swissprot;acc:p10643] C7
3065 wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880] WISP3
3066 vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692] VEGFA
3067 retinoic acid receptor rxr-beta. [swissprot;acc:p28702] no value
3068 headcase homolog; hhdc for homolog of drosophila headcase. [refseq;acc:nm_016217] HECA
3069 bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] BMP5
3070 mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487] MDGA1
3071 serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271] STK38
3072 pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [refseq;acc:nm_017906] PAK1IP1
3073 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] RWDD1
3074 tu12b1-ty protein. [refseq;acc:nm_016575] NT5DC3
3075 ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974] USP5
3076 placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128] no value
3077 h2a histone family, member j isoform 1. [refseq;acc:nm_018267] H2AFJ
3078 camp responsive element binding protein-like 2. [refseq;acc:nm_001310] CREBL2
3079 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] CYP27B1
3080 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] no value
3081 nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489] PTPMT1
3082 alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] CRYAB
3083 glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [swissprot;acc:p48167] GLRB
3084 mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4] MAP2K1IP1
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

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/