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 Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2182 to 2231 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
546 ATP5D atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Squared 27162.5 32347.5 1.19089
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Ranked 207.222 194.262 1.06671
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Measured 4052.77 4612.54 1.13812
547 CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Ranked 207.26 194.346 1.06645
GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Rooted 66.082 71.6525 1.0843
MAT2A s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Squared 25945.4 30892.3 1.19067
WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Measured 5291.92 6020.19 1.13762
548 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Ranked 207.26 194.346 1.06645
FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Measured 8268.19 9405.85 1.13759
GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Rooted 66.082 71.6525 1.0843
VAMP2 vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Squared 27516.2 32720 1.18912
549 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked 207.26 194.346 1.06645
DPM1 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Measured 5865.79 6671.23 1.13731
JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Rooted 66.082 71.6526 1.0843
VAMP1 vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Squared 27516.2 32720 1.18912
550 GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Rooted 66.082 71.6525 1.0843
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Ranked 207.26 194.346 1.06645
PHB prohibitin. [swissprot;acc:p35232] Measured 5773.45 6563.69 1.13687
VAMP4 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Squared 27516.2 32720 1.18912
551 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Measured 5773.45 6563.69 1.13687
CDIPT cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Squared 27516.2 32720 1.18912
GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Rooted 66.082 71.6525 1.0843
GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Ranked 207.261 194.347 1.06645
552 ARFGAP1 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Squared 27516.2 32720 1.18912
CRKL crk-like protein. [swissprot;acc:p46109] Ranked 207.26 194.346 1.06645
CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured 15427.2 13572.8 1.13663
NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Rooted 66.082 71.6523 1.08429
553 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Measured 3853.64 4379.71 1.13651
ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Ranked 207.26 194.346 1.06645
PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Rooted 66.082 71.6523 1.08429
VAMP3 vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Squared 27516.2 32720 1.18912
554 CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured 14830.5 13050.3 1.13641
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Ranked 207.26 194.346 1.06645
HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Rooted 66.0829 71.6462 1.08419
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Squared 8426.68 10010.8 1.18799
555 FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Ranked 207.26 194.346 1.06645
PRPF3 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Rooted 59.7823 64.7895 1.08376
SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 6167.93 7007.7 1.13615
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] Squared 8426.68 10010.8 1.18799
556 CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Rooted 66.0911 71.6061 1.08345
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Ranked 207.27 194.368 1.06638
FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Squared 8426.68 10010.8 1.18799
MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Measured 6167.93 7007.7 1.13615
557 CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Squared 8426.68 10010.8 1.18799
CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Ranked 207.272 194.371 1.06637
INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Measured 6167.93 7007.7 1.13615
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Rooted 97.1967 105.302 1.08339
558 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Ranked 135.087 144.041 1.06628
CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Rooted 66.1583 71.6729 1.08335
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Squared 8426.68 10010.8 1.18799

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/