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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2175 to 2224 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
544 INPP4A Ranked inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] 222.156 208.201 1.06703
IPO11 Squared ran binding protein 11. [refseq;acc:nm_016338] 26018.9 30994.1 1.19121
545 AKT2 Measured rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] 3889.27 4426.74 1.13819
EIF6 Ranked eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 248.866 233.287 1.06678
FAM57A Squared membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 26010 30981.7 1.19115
GABRG2 Rooted gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 66.082 71.6526 1.0843
546 no value interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
ATP5D Squared atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 27162.5 32347.5 1.19089
WAS Ranked wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 207.222 194.262 1.06671
ZNF593 Measured zinc finger protein t86. [swissprot;acc:o00488] 4052.77 4612.54 1.13812
547 CRK Ranked proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 207.26 194.346 1.06645
GABRA4 Rooted gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 66.082 71.6525 1.0843
MAT2A Squared s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 25945.4 30892.3 1.19067
WRNIP1 Measured werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 5291.92 6020.19 1.13762
548 ABL2 Ranked tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 207.26 194.346 1.06645
FDX1 Measured adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
GABRE Rooted gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 66.082 71.6525 1.0843
VAMP2 Squared vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 27516.2 32720 1.18912
549 no value Ranked proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 207.26 194.346 1.06645
DPM1 Measured 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] 5865.79 6671.23 1.13731
JMJD6 Rooted phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 66.082 71.6526 1.0843
VAMP1 Squared vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 27516.2 32720 1.18912
550 GABRA1 Rooted gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 66.082 71.6525 1.0843
HCK Ranked tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 207.26 194.346 1.06645
PHB Measured prohibitin. [swissprot;acc:p35232] 5773.45 6563.69 1.13687
VAMP4 Squared vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] 27516.2 32720 1.18912
551 no value Measured repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 5773.45 6563.69 1.13687
CDIPT Squared cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 27516.2 32720 1.18912
GABRA3 Rooted gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 66.082 71.6525 1.0843
GRAP2 Ranked 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] 207.261 194.347 1.06645
552 ARFGAP1 Squared 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] 27516.2 32720 1.18912
CRKL Ranked crk-like protein. [swissprot;acc:p46109] 207.26 194.346 1.06645
CSTF2 Measured cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 15427.2 13572.8 1.13663
NDUFA6 Rooted nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 66.082 71.6523 1.08429
553 no value Measured tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 3853.64 4379.71 1.13651
ABL1 Ranked proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 207.26 194.346 1.06645
PDXDC1 Rooted similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 66.082 71.6523 1.08429
VAMP3 Squared vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] 27516.2 32720 1.18912
554 CLP1 Measured pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 14830.5 13050.3 1.13641
FYN Ranked proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 207.26 194.346 1.06645
HOXD9 Rooted homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 66.0829 71.6462 1.08419
PSEN2 Squared presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 8426.68 10010.8 1.18799
555 FGR Ranked proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 207.26 194.346 1.06645
PRPF3 Rooted u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 59.7823 64.7895 1.08376
SEPHS2 Measured selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 6167.93 7007.7 1.13615
SKP1A Squared 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] 8426.68 10010.8 1.18799
556 CBLB Rooted signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 66.0911 71.6061 1.08345
CUTL1 Ranked ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 207.27 194.368 1.06638
FBXW7 Squared 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] 8426.68 10010.8 1.18799
MICAL2 Measured flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 6167.93 7007.7 1.13615

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/