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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2180 to 2229 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
545 Rooted gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 66.082 71.6526 1.0843
546 Measured zinc finger protein t86. [swissprot;acc:o00488] 4052.77 4612.54 1.13812
Ranked wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 207.222 194.262 1.06671
Squared atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 27162.5 32347.5 1.19089
Rooted interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 66.082 71.6526 1.0843
547 Measured werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 5291.92 6020.19 1.13762
Ranked proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 207.26 194.346 1.06645
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
Rooted gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 66.082 71.6525 1.0843
548 Measured adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
Ranked tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 207.26 194.346 1.06645
Squared vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 27516.2 32720 1.18912
Rooted gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 66.082 71.6525 1.0843
549 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
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
Squared vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 27516.2 32720 1.18912
Rooted phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 66.082 71.6526 1.0843
550 Measured prohibitin. [swissprot;acc:p35232] 5773.45 6563.69 1.13687
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
Squared vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] 27516.2 32720 1.18912
Rooted gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 66.082 71.6525 1.0843
551 Measured repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 5773.45 6563.69 1.13687
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
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
Rooted gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 66.082 71.6525 1.0843
552 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
Ranked crk-like protein. [swissprot;acc:p46109] 207.26 194.346 1.06645
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
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 Measured tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 3853.64 4379.71 1.13651
Ranked proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 207.26 194.346 1.06645
Squared vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] 27516.2 32720 1.18912
Rooted similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 66.082 71.6523 1.08429
554 Measured pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 14830.5 13050.3 1.13641
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
Squared presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 8426.68 10010.8 1.18799
Rooted homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 66.0829 71.6462 1.08419
555 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
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
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
Rooted u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 59.7823 64.7895 1.08376
556 Measured flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 6167.93 7007.7 1.13615
Ranked ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 207.27 194.368 1.06638
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
Rooted signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 66.0911 71.6061 1.08345
557 Measured inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 6167.93 7007.7 1.13615
Ranked homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 207.272 194.371 1.06637
Squared cullin homolog 2 (cul-2). [swissprot;acc:q13617] 8426.68 10010.8 1.18799
Rooted t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 97.1967 105.302 1.08339
558 Measured selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 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
- 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/