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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2230 to 2279 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
558 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Squared 8426.68 10010.8 1.18799
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Measured 6167.93 7007.7 1.13615
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Ranked 135.087 144.041 1.06628
559 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Squared 8426.68 10010.8 1.18799
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Rooted 62.7397 67.9651 1.08329
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] Measured 6167.93 7007.7 1.13615
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Ranked 207.309 194.452 1.06612
560 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Measured 5480.24 6222.04 1.13536
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] Squared 26334.7 31272.3 1.18749
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Rooted 51.0687 47.1439 1.08325
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Ranked 205.74 193.021 1.06589
561 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Rooted 62.7424 67.9648 1.08324
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Ranked 205.89 193.183 1.06578
transforming protein rhoc (h9). [swissprot;acc:p08134] Measured 5480.24 6222.04 1.13536
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Squared 18240.1 21659.2 1.18745
562 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Rooted 62.7424 67.9648 1.08324
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Squared 25294.9 30027.4 1.18709
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Ranked 220.744 207.121 1.06577
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Measured 5480.24 6222.04 1.13536
563 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
calcyphosine. [swissprot;acc:q13938] Ranked 220.744 207.121 1.06577
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] Rooted 62.7424 67.9648 1.08324
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Squared 30408.3 36092.8 1.18694
564 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
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Ranked 220.744 207.121 1.06577
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Rooted 62.7424 67.9648 1.08324
transforming protein rhoa (h12). [swissprot;acc:p06749] Measured 5480.24 6222.04 1.13536
565 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Squared 25287.7 30003.7 1.18649
limkain b1. [refseq;acc:nm_019081] Rooted 62.7424 67.9648 1.08324
sedlin. [swissprot;acc:o14582] Ranked 129.219 121.261 1.06563
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured 10434.4 11846.2 1.1353
566 autoantigen ngp-1. [swissprot;acc:q13823] 3766.14 4274.79 1.13506
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Rooted 62.7424 67.9648 1.08324
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Ranked 129.219 121.261 1.06563
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Squared 34268.1 40650.4 1.18625
567 bet3 homolog. [swissprot;acc:o43617] Ranked 129.219 121.261 1.06563
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Rooted 62.7424 67.9648 1.08324
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Measured 10264.9 9043.51 1.13506
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Squared 34219.8 40585.4 1.18602
568 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Rooted 62.7424 67.9648 1.08324
grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Measured 4134.77 4691.24 1.13458
max protein. [swissprot;acc:p25912] Squared 18764.5 22255 1.18602
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Ranked 226.3 212.38 1.06554
569 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Measured 4134.77 4691.24 1.13458
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted 62.7424 67.9648 1.08324
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Squared 52623.3 44380.3 1.18574
t54 protein. [swissprot;acc:q92917] Ranked 226.3 212.38 1.06554
570 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Rooted 62.7424 67.9648 1.08324
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Squared 52623.3 44380.3 1.18574
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Ranked 229.709 215.631 1.06529

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/