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.


Navigation/Query Panel:
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 Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2625 to 2674 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
657 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Subtracted Low confidence 207.03 201.339 5.691
GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] High confidence 214.256 202.14 12.116
ITGB7 integrin beta-7 precursor. [swissprot;acc:p26010] Divided Low confidence 206.341 200.609 1.02857
SYN3 synapsin iii. [swissprot;acc:o14994] High confidence 229.072 216.576 1.0577
658 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
ARFGEF1 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Subtracted Low confidence 203.293 197.621 5.672
GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] High confidence 214.256 202.14 12.116
ITGB3 integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Divided Low confidence 206.342 200.61 1.02857
659 DHODH dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Subtracted 203.975 198.304 5.671
GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] High confidence 214.256 202.14 12.116
HEY1 hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Divided 229.072 216.576 1.0577
TP53I3 tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Low confidence 175.504 170.633 1.02855
660 ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] High confidence 229.072 216.576 1.0577
GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Subtracted 214.256 202.14 12.116
ITGA7 integrin alpha-7 precursor. [swissprot;acc:q13683] Divided Low confidence 206.32 200.601 1.02851
SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 204.882 199.214 5.668
661 ARFGEF2 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 203.283 197.617 5.666
GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] High confidence 214.256 202.14 12.116
HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Divided 229.072 216.576 1.0577
SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Low confidence 200.62 195.059 1.02851
662 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 206.115 200.462 5.653
GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] High confidence 214.256 202.14 12.116
ITGA6 integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229] Divided Low confidence 206.321 200.601 1.02851
SYN2 synapsin ii. [swissprot;acc:q92777] High confidence 229.072 216.576 1.0577
663 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Subtracted Low confidence 204.551 198.901 5.65
ITGA3 integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] Divided 206.32 200.601 1.02851
MRRF mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] High confidence 229.072 216.576 1.0577
NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Subtracted 214.256 202.141 12.115
664 AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Low confidence 191.507 185.859 5.648
PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] High confidence 214.256 202.141 12.115
PEX5 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Divided 229.072 216.576 1.0577
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Low confidence 201.821 196.233 1.02848
665 HEY2 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] High confidence 229.072 216.576 1.0577
HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Subtracted 214.254 202.166 12.088
PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Low confidence 204.81 199.174 5.636
SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Divided 204.882 199.214 1.02845
666 CYP3A43 cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] Subtracted 203.712 198.082 5.63
EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] High confidence 250.465 238.38 12.085
HES1 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Divided 229.072 216.576 1.0577
SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Low confidence 200.639 195.092 1.02843
667 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted High confidence 250.465 238.38 12.085
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Low confidence 213.926 208.315 5.611
ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Divided High confidence 229.072 216.576 1.0577
RNF144B ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Low confidence 208.62 202.855 1.02842
668 ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] High confidence 229.072 216.576 1.0577
CYP3A7 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Subtracted Low confidence 203.727 198.116 5.611
FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] High confidence 244.495 232.419 12.076
MIOX inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [swissprot;acc:q9ugb7] Divided Low confidence 212.062 206.202 1.02842
669 no value presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Subtracted High confidence 232.601 244.534 11.933
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Low confidence 213.929 208.318 5.611

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/