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 Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1918 to 1967 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
480 CDS1 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
CHRNA2 Measured neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 11053.5 1.14549
NETO2 Ranked neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
481 no value Rooted histone h2b. [refseq;acc:nm_175055] 50.6084 55.2961 1.09263
MAPKAPK3 Measured mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 1.14549
NETO1 Ranked neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
SRP9 Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16335.9 19660.7 1.20353
482 no value Rooted histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
HNRNPU Ranked heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
MAPK14 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
SLC13A3 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
483 no value Rooted histone h2b.d (h2b/d). [swissprot;acc:q99877] 50.6084 55.2961 1.09263
CHRNA4 Measured neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 11053.5 1.14549
RUNX2 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
SLC13A2 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
484 CHRNA3 Measured neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 9649.61 11053.5 1.14549
HIST3H3 Rooted histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 50.6084 55.2961 1.09263
HNRPUL1 Ranked e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 237.109 254.667 1.07405
SLC13A4 Squared solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 26867.2 32335 1.20351
485 HIST1H2BA Rooted testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 50.6084 55.2961 1.09263
RPL18 Ranked 60s ribosomal protein l18. [swissprot;acc:q07020] 237.109 254.667 1.07405
SLC13A1 Squared solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 26867.2 32335 1.20351
SPHK2 Measured sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 9649.61 11053.5 1.14549
486 no value Rooted histone h2b.e (h2b/e). [swissprot;acc:q99879] 50.6084 55.2961 1.09263
CLEC11A 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
MCTS1 Ranked mct-1 protein. [refseq;acc:nm_014060] 226.313 243.03 1.07387
SCAMP2 Squared secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 26865.9 32332.9 1.20349
487 no value Rooted tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 50.0015 54.627 1.09251
MRPL22 Ranked mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] 226.313 243.03 1.07387
PYCR2 Measured pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 5277.4 6042.88 1.14505
SCAMP3 Squared secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 26865.9 32332.9 1.20349
488 CLEC3A Measured c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 10872.4 12447 1.14483
POLR3A Rooted dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 50.4315 46.1703 1.09229
SART1 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
SCAMP1 Squared secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 26866.1 32333.2 1.20349
489 CDS2 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
MRPL12 Rooted 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 50.5505 46.2797 1.09228
PPM1B Ranked protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 1.07257
PYCR1 Measured pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 5281.11 6044.61 1.14457
490 ARHGEF7 Ranked rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 236.015 1.0719
FOXP4 Squared forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 5301.97 6377.93 1.20294
NUDT12 Rooted nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 50.5505 46.2797 1.09228
PPP1R13B Measured protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 15274.9 13346.9 1.14445
491 FOXP1 Squared forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 5302.25 6378.24 1.20293
GTPBP4 Ranked nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 251.83 234.951 1.07184
NAV2 Measured 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] 5980.15 6843.48 1.14437
PARK2 Rooted parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 55.1759 60.2621 1.09218
492 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
FOXP3 Squared forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 5313 6389.9 1.20269
NAV1 Measured neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 5979.94 6842.76 1.14429

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/