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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1908 to 1957 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
477 Rooted inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] 62.574 68.4128 1.09331
478 Measured star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 11053.5 1.14549
Ranked transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 228.051 212.321 1.07409
Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16318.4 19645.8 1.2039
Rooted histone h2b.c (h2b/c). [swissprot;acc:q99880] 50.6084 55.2961 1.09263
479 Measured star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 9649.61 11053.5 1.14549
Ranked nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 228.051 212.321 1.07409
Squared translation initiation factor if-2. [swissprot;acc:o60841] 24031.6 28929.7 1.20382
Rooted histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 50.6084 55.2961 1.09263
480 Measured neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 11053.5 1.14549
Ranked neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
Squared phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 26874.6 32347.4 1.20364
Rooted histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 50.6084 55.2961 1.09263
481 Measured mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 1.14549
Ranked neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16335.9 19660.7 1.20353
Rooted histone h2b. [refseq;acc:nm_175055] 50.6084 55.2961 1.09263
482 Measured mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] 9649.61 11053.5 1.14549
Ranked heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
Squared solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] 26867.3 32335.2 1.20352
Rooted histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
483 Measured neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 11053.5 1.14549
Ranked 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] 237.109 254.667 1.07405
Squared solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 26867.3 32335.2 1.20352
Rooted histone h2b.d (h2b/d). [swissprot;acc:q99877] 50.6084 55.2961 1.09263
484 Measured neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 9649.61 11053.5 1.14549
Ranked e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 237.109 254.667 1.07405
Squared solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 26867.2 32335 1.20351
Rooted histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 50.6084 55.2961 1.09263
485 Measured sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 9649.61 11053.5 1.14549
Ranked 60s ribosomal protein l18. [swissprot;acc:q07020] 237.109 254.667 1.07405
Squared solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 26867.2 32335 1.20351
Rooted testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 50.6084 55.2961 1.09263
486 Measured stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 10908.6 12491.8 1.14513
Ranked mct-1 protein. [refseq;acc:nm_014060] 226.313 243.03 1.07387
Squared secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 26865.9 32332.9 1.20349
Rooted histone h2b.e (h2b/e). [swissprot;acc:q99879] 50.6084 55.2961 1.09263
487 Measured pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 5277.4 6042.88 1.14505
Ranked mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] 226.313 243.03 1.07387
Squared secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 26865.9 32332.9 1.20349
Rooted tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 50.0015 54.627 1.09251
488 Measured c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 10872.4 12447 1.14483
Ranked 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] 225.026 209.798 1.07258
Squared secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 26866.1 32333.2 1.20349
Rooted dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 50.4315 46.1703 1.09229
489 Measured pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 5281.11 6044.61 1.14457
Ranked protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 1.07257
Squared 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] 26859 32321.2 1.20337
Rooted 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 50.5505 46.2797 1.09228
490 Measured protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 15274.9 13346.9 1.14445

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/