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 12314 to 12363 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1038 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Squared Divided 31994 36719.6 1.1477
elks protein. [refseq;acc:nm_015064] Ranked Subtracted 218.162 211.648 6.514
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Rooted Divided 60.6801 63.8644 1.05248
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Measured 5417.95 5924.41 1.09348
pbk1 protein. [sptrembl;acc:o76021] Rooted Subtracted 51.7294 55.0405 3.3111
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Measured 5910.54 6440.58 530.04
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Squared 26403.8 29786.4 3382.6
1039 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Ranked Divided 207.719 214.236 1.03137
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Squared 31994 36719.6 1.1477
myb-related protein b (b-myb). [swissprot;acc:p10244] Measured 5418.92 5923.09 1.09304
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Squared Subtracted 22827.7 26208.2 3380.5
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Ranked 220.118 213.685 6.433
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Rooted 56.264 59.5672 3.3032
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided 60.6801 63.8644 1.05248
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Measured Subtracted 5719.01 6248.6 529.59
1040 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Ranked 220.118 213.685 6.433
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Rooted 56.264 59.5672 3.3032
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Squared Divided 31994 36719.6 1.1477
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Subtracted 22827.7 26208.2 3380.5
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Measured 5719.01 6248.6 529.59
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Divided 5421.93 5926.08 1.09298
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Rooted 60.6801 63.8644 1.05248
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Ranked 163.24 168.359 1.03136
1041 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Subtracted 220.118 213.685 6.433
dead-box protein. [refseq;acc:nm_018665] Measured 5719.01 6248.6 529.59
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Squared Divided 31994 36719.6 1.1477
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Ranked 186.774 181.099 1.03134
interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Rooted 61.7511 64.9897 1.05245
myb-related protein a (a-myb). [swissprot;acc:p10243] Measured 5419.18 5922.84 1.09294
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Squared Subtracted 21086.3 24464.1 3377.8
wd-repeat protein bing4. [swissprot;acc:o15213] Rooted 51.7527 55.0117 3.259
1042 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided 60.9639 64.1576 1.05239
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Squared 31994 36719.6 1.1477
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Ranked 186.799 181.127 1.03132
histone h2b.c (h2b/c). [swissprot;acc:q99880] Measured Subtracted 3946.32 4475.47 529.15
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Squared 30908.9 34282.7 3373.8
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Measured Divided 5887.52 6434.32 1.09287
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Rooted Subtracted 86.1912 82.9401 3.2511
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Ranked 216.901 210.485 6.416
1043 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Divided 187.834 182.137 1.03128
15 kda selenoprotein precursor. [swissprot;acc:o60613] Measured 6344.41 6933.36 1.09283
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Rooted Subtracted 86.1912 82.9401 3.2511
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Squared Divided 31989.3 36713.2 1.14767
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Subtracted 30908.9 34282.7 3373.8
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured 3946.32 4475.47 529.15
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Ranked 239.219 232.837 6.382
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Rooted Divided 59.0741 62.1501 1.05207
1044 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] Ranked Subtracted 269.157 275.531 6.374
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Rooted Divided 65.4147 68.8149 1.05198
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Subtracted 86.1912 82.9401 3.2511

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/