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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank description Gene Network Comparison Type Value Type Hugo Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2975 to 3024 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Hugo
Interaction Map
red
green
network_comparison
186 tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Divided Rooted TPM1 Low confidence 70.7466 75.1547 1.06231
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Subtracted SNRPB2 70.6712 75.0934 4.4222
187 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Squared NONO High confidence 71383 57399.3 13983.7
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Ranked CRYAB Low confidence 219.543 208.868 10.675
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided Measured ALG1 9012.1 8376.35 1.0759
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Rooted ATG4B High confidence 153.548 133.153 1.15317
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Subtracted Measured DAD1 Low confidence 6893.42 7491.39 597.97
dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Divided Rooted DUOX2 69.8853 74.201 1.06175
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Squared HS3ST3B1 High confidence 41502.9 30836.8 1.34589
mosaic protein lgn. [swissprot;acc:p81274] Subtracted Rooted GPSM2 47.6504 36.9304 10.72
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided Ranked REV1 226.582 198.444 1.14179
Subtracted Measured 4366.44 5899.76 1533.32
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided Ranked no value Low confidence 189.373 179.829 1.05307
serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Squared MAK 45399.1 50379.1 1.10969
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Measured SNRPD3 High confidence 4569.48 5885.79 1.28807
sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] Subtracted Squared ATP1B2 Low confidence 52543.2 47411.7 5131.5
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Ranked SNX13 High confidence 227.357 254.15 26.793
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Rooted TPM3 Low confidence 70.7318 75.1524 4.4206
188 alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] Divided Measured AADAT 9986.51 10741.3 1.07558
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted Ranked GSTO2 High confidence 227.357 254.15 26.793
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] CYC1 Low confidence 208.591 219.23 10.639
dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Divided Rooted DUOX1 69.8912 74.2044 1.06171
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Squared HS3ST2 High confidence 41502.9 30836.8 1.34589
paraspeckle protein 1. [refseq;acc:nm_018282] Subtracted PSPC1 71360.3 57385.8 13974.5
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided Ranked PRMT1 226.582 198.444 1.14179
Subtracted Measured 4366.44 5899.76 1533.32
ras-related protein rab-26. [swissprot;acc:q9ulw5] RAB26 Low confidence 10765.1 10174.7 590.4
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted RGS17 High confidence 47.6504 36.9304 10.72
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Divided Ranked RPS6KC1 Low confidence 189.45 179.944 1.05283
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Measured STT3B High confidence 4571.89 5864.86 1.28281
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Rooted E2F1 46.0352 53.0192 1.15171
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Squared KRAS Low confidence 51551.5 46457.1 1.10966
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Subtracted Rooted TPM1 70.7466 75.1547 4.4081
x/potassium-transporting atpase beta-m chain (x,k-atpase beta-m subunit). [swissprot;acc:q9un42] Squared ATP1B4 52525.1 47402.9 5122.2
189 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked STAMBPL1 196.362 206.979 10.617
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Divided DNALI1 214.779 204.039 1.05264
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Squared CENPJ 65169.1 58753.9 1.10919
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 Ranked PCYT1A High confidence 241.373 267.352 25.979
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Divided Rooted DGAT1 Low confidence 69.9065 74.2132 1.06161
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Subtracted GNAO1 High confidence 47.6504 36.9304 10.72
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided Squared DCPS 41502.9 30836.8 1.34589
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Subtracted Measured NDUFA12 Low confidence 5811.84 6399.42 587.58
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Divided SLC11A1 6933.47 7456.24 1.0754
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted Rooted NUBP2 69.7469 74.1228 4.3759
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided Measured STT3A High confidence 4571.89 5864.86 1.28281
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked PRMT8 226.582 198.444 1.14179
Subtracted Measured 4366.44 5899.76 1533.32
sodium/potassium-transporting atpase beta-3 chain (sodium/potassium- dependent atpase beta-3 subunit) (atpb-3). [swissprot;acc:p54709] Squared ATP1B3 Low confidence 52520.9 47400.8 5120.1
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] SFPQ High confidence 70694.1 56989.9 13704.2
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided Rooted E2F2 46.0352 53.0192 1.15171

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/