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 2208 to 2257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
552 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
557 CUL2 Squared cullin homolog 2 (cul-2). [swissprot;acc:q13617] 8426.68 10010.8 1.18799
CUTL2 Ranked homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 207.272 194.371 1.06637
INPP4B 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
TCP1 Rooted t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 97.1967 105.302 1.08339
558 no value Ranked ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 135.087 144.041 1.06628
CBL Rooted cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 66.1583 71.6729 1.08335
PSEN1 Squared presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 8426.68 10010.8 1.18799
SEPHS1 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
559 CUL1 Squared cullin homolog 1 (cul-1). [swissprot;acc:q13616] 8426.68 10010.8 1.18799
FTH1 Rooted ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 62.7397 67.9651 1.08329
INPP4A Measured 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] 6167.93 7007.7 1.13615
WASL Ranked neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 207.309 194.452 1.06612
560 no value Rooted putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 51.0687 47.1439 1.08325
CBS Measured cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 5480.24 6222.04 1.13536
ETFDH Squared electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] 26334.7 31272.3 1.18749
SOS1 Ranked son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] 205.74 193.021 1.06589
561 CREG2 Rooted cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 62.7424 67.9648 1.08324
LSM8 Squared u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 18240.1 21659.2 1.18745
RHOC Measured transforming protein rhoc (h9). [swissprot;acc:p08134] 5480.24 6222.04 1.13536
SOS2 Ranked son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 205.89 193.183 1.06578
562 no value Rooted dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 62.7424 67.9648 1.08324
FBP2 Squared fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 25294.9 30027.4 1.18709
GULP1 Ranked ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 220.744 207.121 1.06577
TST Measured thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 5480.24 6222.04 1.13536
563 CAPS Ranked calcyphosine. [swissprot;acc:q13938] 220.744 207.121 1.06577
DLGAP1 Rooted disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] 62.7424 67.9648 1.08324
MPST Measured 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 5480.24 6222.04 1.13536
WIPF1 Squared wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] 30408.3 36092.8 1.18694
564 AHCYL1 Rooted putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 62.7424 67.9648 1.08324
CAD Squared cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 25396.2 30143.4 1.18693
CRNKL1 Ranked crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 220.744 207.121 1.06577
RHOA Measured transforming protein rhoa (h12). [swissprot;acc:p06749] 5480.24 6222.04 1.13536
565 FBP1 Squared fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 25287.7 30003.7 1.18649

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/