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.


Navigation/Query Panel:
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 1930 to 1979 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
483 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Measured 9649.61 11053.5 1.14549
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Ranked 237.109 254.667 1.07405
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Squared 26867.3 32335.2 1.20352
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Ranked 237.109 254.667 1.07405
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Rooted 50.6084 55.2961 1.09263
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Measured 9649.61 11053.5 1.14549
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Squared 26867.2 32335 1.20351
485 60s ribosomal protein l18. [swissprot;acc:q07020] Ranked 237.109 254.667 1.07405
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Squared 26867.2 32335 1.20351
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Measured 9649.61 11053.5 1.14549
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Rooted 50.6084 55.2961 1.09263
486 histone h2b.e (h2b/e). [swissprot;acc:q99879]
mct-1 protein. [refseq;acc:nm_014060] Ranked 226.313 243.03 1.07387
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Squared 26865.9 32332.9 1.20349
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Measured 10908.6 12491.8 1.14513
487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Ranked 226.313 243.03 1.07387
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Measured 5277.4 6042.88 1.14505
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared 26865.9 32332.9 1.20349
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Rooted 50.0015 54.627 1.09251
488 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Measured 10872.4 12447 1.14483
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Rooted 50.4315 46.1703 1.09229
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Squared 26866.1 32333.2 1.20349
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] Ranked 225.026 209.798 1.07258
489 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Rooted 50.5505 46.2797 1.09228
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Squared 26859 32321.2 1.20337
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Ranked 231.276 215.627 1.07257
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Measured 5281.11 6044.61 1.14457
490 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Squared 5301.97 6377.93 1.20294
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Rooted 50.5505 46.2797 1.09228
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured 15274.9 13346.9 1.14445
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Ranked 220.183 236.015 1.0719
491 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Squared 5302.25 6378.24 1.20293
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Measured 5980.15 6843.48 1.14437
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Ranked 251.83 234.951 1.07184
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Rooted 55.1759 60.2621 1.09218
492 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Squared 5313 6389.9 1.20269
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Rooted 55.1759 60.2621 1.09218
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured 5979.94 6842.76 1.14429
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Ranked 220.171 235.979 1.0718
493 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Rooted 55.1759 60.2621 1.09218
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked 220.172 235.98 1.0718
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Measured 5979.95 6842.78 1.14429
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Squared 28408.7 34148.5 1.20204
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Measured 5979.93 6842.72 1.14428
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 1.20082
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Rooted 55.1759 60.2621 1.09218
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked 220.172 235.98 1.0718
495 60s ribosomal protein l8. [swissprot;acc:p25120] Rooted 55.1759 60.2621 1.09218
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared 30286.5 36362 1.2006
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Ranked 220.171 235.979 1.0718

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/