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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Gene Value Type Rank description Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 77072 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
green
930 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Divided Low confidence 7928.24 1.039 8237.48
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted High confidence 6281.21 556.4 6837.61
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Low confidence 7948.13 312.69 8260.82
931 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] Divided 7637.56 1.03899 7935.35
cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Subtracted High confidence 6281.21 556.4 6837.61
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Low confidence 7948.13 312.69 8260.82
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided High confidence 5638.59 1.09853 6194.17
932 acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] Low confidence 7637.56 1.03899 7935.35
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted High confidence 6281.21 556.4 6837.61
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Low confidence 8059.35 312.55 8371.9
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Divided High confidence 5638.46 1.09853 6194.04
933 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Subtracted Low confidence 8358.82 312.52 8671.34
acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] Divided 7637.56 1.03899 7935.35
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Subtracted High confidence 6281.21 556.4 6837.61
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 5638.46 1.09853 6194.04
934 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Subtracted Low confidence 8005.86 312.41 8318.27
general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Divided 7637.56 1.03899 7935.35
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Subtracted High confidence 6281.21 556.4 6837.61
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Divided 5640 1.0985 6195.52
935 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] Low confidence 7637.56 1.03899 7935.35
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Subtracted 7273.8 312.38 7586.18
homolog of yeast maf1. [refseq;acc:nm_032272] High confidence 6133.83 556.35 6690.18
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Divided 5413.63 1.09842 5946.46
936 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] Low confidence 7637.56 1.03899 7935.35
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Subtracted 8059.5 312.33 8371.83
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Divided High confidence 5628.21 1.09811 6180.37
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Subtracted 6133.83 556.35 6690.18
937 metaxin 1. [swissprot;acc:q13505] Low confidence 8387.04 312.2 8699.24
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Divided High confidence 5859.25 1.09776 6432.03
protein x 0001. [refseq;acc:nm_016302] Low confidence 8214.28 1.03895 8534.22
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Subtracted High confidence 6133.83 556.35 6690.18
938 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Divided 5859.25 1.09776 6432.03
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Low confidence 7751.77 1.03891 8053.37
transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] Subtracted 8020.09 312 8332.09
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] High confidence 6133.83 556.35 6690.18
939 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Divided Low confidence 8454.45 1.0389 8783.33
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] High confidence 5859.25 1.09776 6432.03
transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754] Subtracted Low confidence 8020.09 312 8332.09
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Divided High confidence 5568.96 1.09775 6113.35
nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] Low confidence 7569.42 1.0389 7863.85
transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] Subtracted 8020.09 312 8332.09
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] High confidence 6280.74 556.27 6837.01
941 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Divided 4970.21 1.09761 5455.34
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Subtracted Low confidence 8153.64 311.96 8465.6
paraspeckle protein 1. [refseq;acc:nm_018282] High confidence 10241.3 556.09 9685.21
transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] Divided Low confidence 8020.09 1.0389 8332.09
942 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 8454.45 8783.33
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] High confidence 6597.56 1.09747 7240.64
sipl protein. [refseq;acc:nm_018269] Subtracted Low confidence 8280.28 311.43 8591.71

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/