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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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 Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 777 to 826 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
389 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Low confidence 8159.97 8595.12 1.05333
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] High confidence 4533.74 5279.4 1.16447
390 rw1 protein (fragment). [swissprot;acc:q92545]
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Low confidence 6983.51 7354.87 1.05318
391 tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] High confidence 3658.76 3144.39 1.16358
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Low confidence 8552.2 9004.53 1.05289
392 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] High confidence 3641.89 4236.95 1.16339
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Low confidence 7781.34 8192.41 1.05283
393 cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] 8673.83 9132.05
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] High confidence 4490.28 5222.25 1.16301
394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Low confidence 7679.4 8084.79 1.05279
395 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 8552.34 9003.72 1.05278
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] High confidence 4532.73 5269.33 1.16251
396 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Low confidence 7680.02 8085.19 1.05276
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] High confidence 6563.65 7627.29 1.16205
397 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Low confidence 7679.55 8084.63 1.05275
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] High confidence 5367.04 6233.12 1.16137
398 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Low confidence 7680.47 8085.46 1.05273
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] High confidence 5084.26 5904.1 1.16125
399 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Low confidence 7680.62 8085.57 1.05272
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] High confidence 5201.41 4479.76 1.16109
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
mad protein (max dimerizer). [swissprot;acc:q05195] Low confidence 6970.25 7337.73 1.05272
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 5201.41 4479.76 1.16109
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Low confidence 10800.7 10260 1.0527
402 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 5201.41 4479.76 1.16109
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Low confidence 7934.21 8352.26 1.05269
403 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] High confidence 5201.41 4479.76 1.16109
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Low confidence 8853.13 9319.56 1.05269
404 kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] 10008.8 9508.16 1.05265
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 5201.41 4479.76 1.16109
405 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Low confidence 10008.8 9508.16 1.05265
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 5201.41 4479.76 1.16109
406 l-lactate dehydrogenase a-like (ec 1.1.1.27). [swissprot;acc:q9byz2] Low confidence 6973.3 7340.34 1.05264
thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 5201.41 4479.76 1.16109
407 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Low confidence 6634.26 6983.5 1.05264
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] High confidence 6603.41 7664.65 1.16071
408 dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 1.1604
l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [swissprot;acc:p07864] Low confidence 6973.31 7340.35 1.05263
409 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] High confidence 6102.59 7081.46 1.1604
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 6973.32 7340.36 1.05263
410 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] High confidence 6102.59 7081.46 1.1604
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Low confidence 6973.61 7340.61 1.05263
411 l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195] 6973.35 7340.39
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] High confidence 6102.59 7081.46 1.1604
412 clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] Low confidence 6973.35 7340.39 1.05263
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 3594.31 4169.95 1.16015
413 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Low confidence 6974.82 7341.65 1.05259
vav proto-oncogene. [swissprot;acc:p15498] High confidence 6644.99 7707.8 1.15994

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/