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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2232 to 2281 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
558 SEPHS1 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
559 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Squared 8426.68 10010.8 1.18799
FTH1 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Rooted 62.7397 67.9651 1.08329
INPP4A 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
WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Ranked 207.309 194.452 1.06612
560 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Rooted 51.0687 47.1439 1.08325
CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Measured 5480.24 6222.04 1.13536
ETFDH 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
SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Ranked 205.74 193.021 1.06589
561 CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Rooted 62.7424 67.9648 1.08324
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Squared 18240.1 21659.2 1.18745
RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Measured 5480.24 6222.04 1.13536
SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Ranked 205.89 193.183 1.06578
562 no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Rooted 62.7424 67.9648 1.08324
FBP2 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
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Ranked 220.744 207.121 1.06577
TST thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Measured 5480.24 6222.04 1.13536
563 CAPS calcyphosine. [swissprot;acc:q13938] Ranked 220.744 207.121 1.06577
DLGAP1 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
MPST 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Measured 5480.24 6222.04 1.13536
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Squared 30408.3 36092.8 1.18694
564 AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Rooted 62.7424 67.9648 1.08324
CAD 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] Squared 25396.2 30143.4 1.18693
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Ranked 220.744 207.121 1.06577
RHOA transforming protein rhoa (h12). [swissprot;acc:p06749] Measured 5480.24 6222.04 1.13536
565 FBP1 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
KIAA0430 limkain b1. [refseq;acc:nm_019081] Rooted 62.7424 67.9648 1.08324
SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured 10434.4 11846.2 1.1353
ZNF547 sedlin. [swissprot;acc:o14582] Ranked 129.219 121.261 1.06563
566 no value 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
GNL2 autoantigen ngp-1. [swissprot;acc:q13823] Measured 3766.14 4274.79 1.13506
567 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Squared 34219.8 40585.4 1.18602
CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Rooted 62.7424 67.9648 1.08324
DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Measured 10264.9 9043.51 1.13506
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Ranked 129.219 121.261 1.06563
568 no value putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 226.3 212.38 1.06554
DLGAP3 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
GRPEL2 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Measured 4134.77 4691.24 1.13458
MAX max protein. [swissprot;acc:p25912] Squared 18764.5 22255 1.18602
569 DYNLT3 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 52623.3 44380.3 1.18574
GPKOW t54 protein. [swissprot;acc:q92917] Ranked 226.3 212.38 1.06554
GRPEL1 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Measured 4134.77 4691.24 1.13458
KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted 62.7424 67.9648 1.08324
570 no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
MRE11A double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Squared 52623.3 44380.3 1.18574
SFRS11 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Ranked 229.709 215.631 1.06529
SMARCD2 swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Measured 4134.77 4691.24 1.13458
571 FTL ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Rooted 62.7424 67.9648 1.08324

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/