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.


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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1927 to 1976 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
482 Squared SLC13A3 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 no value histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
483 Measured CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 11053.5 1.14549
Ranked RUNX2 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 SLC13A2 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 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] 50.6084 55.2961 1.09263
484 Measured CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 9649.61 11053.5 1.14549
Ranked HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 237.109 254.667 1.07405
Squared SLC13A4 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 26867.2 32335 1.20351
Rooted HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 50.6084 55.2961 1.09263
485 Measured SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 9649.61 11053.5 1.14549
Ranked RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] 237.109 254.667 1.07405
Squared SLC13A1 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 26867.2 32335 1.20351
Rooted HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 50.6084 55.2961 1.09263
486 Measured CLEC11A 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 MCTS1 mct-1 protein. [refseq;acc:nm_014060] 226.313 243.03 1.07387
Squared SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 26865.9 32332.9 1.20349
Rooted no value histone h2b.e (h2b/e). [swissprot;acc:q99879] 50.6084 55.2961 1.09263
487 Measured PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 5277.4 6042.88 1.14505
Ranked MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] 226.313 243.03 1.07387
Squared SCAMP3 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 26865.9 32332.9 1.20349
Rooted no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 50.0015 54.627 1.09251
488 Measured CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 10872.4 12447 1.14483
Ranked SART1 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 SCAMP1 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 26866.1 32333.2 1.20349
Rooted POLR3A 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 PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 5281.11 6044.61 1.14457
Ranked PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 1.07257
Squared 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
Rooted MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 50.5505 46.2797 1.09228
490 Measured PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 15274.9 13346.9 1.14445
Ranked ARHGEF7 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
Squared FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 5301.97 6377.93 1.20294
Rooted NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 50.5505 46.2797 1.09228
491 Measured NAV2 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
Ranked GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 251.83 234.951 1.07184
Squared FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 5302.25 6378.24 1.20293
Rooted PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 55.1759 60.2621 1.09218
492 Measured NAV1 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
Ranked PAK2 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] 220.171 235.979 1.0718
Squared FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 5313 6389.9 1.20269
Rooted no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 55.1759 60.2621 1.09218
493 Measured NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 5979.95 6842.78 1.14429
Ranked COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 220.172 235.98 1.0718
Squared AGXT serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] 28408.7 34148.5 1.20204
Rooted no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 55.1759 60.2621 1.09218
494 Measured ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 5979.93 6842.72 1.14428
Ranked PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 220.172 235.98 1.0718
Squared ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 31583 37925.6 1.20082
Rooted PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 55.1759 60.2621 1.09218

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/