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 1844 to 1893 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
461 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted High confidence 2353.63 3225.65 872.02
462 histone h1.1. [swissprot;acc:q02539] Low confidence 8780.49 9179.06 398.57
pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5] Divided 8864.53 9309.27 1.05017
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] High confidence 11383.2 9926.61 1.14674
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 2353.63 3225.65 872.02
463 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Divided Low confidence 8844.87 9288.13 1.05011
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] High confidence 3720.18 4264.46 1.1463
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted 2353.63 3225.65 872.02
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Low confidence 7787.16 8185.37 398.21
464 cullin homolog 2 (cul-2). [swissprot;acc:q13617] High confidence 2353.63 3225.65 872.02
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 4858.96 5568.85 1.1461
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Low confidence 7847.59 8240.61 1.05008
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Subtracted 7831.81 8229.98 398.17
465 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] High confidence 2353.63 3225.65 872.02
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Divided Low confidence 7580.97 7960.37 1.05005
thimet oligopeptidase (ec 3.4.24.15) (endopeptidase 24.15) (mp78). [swissprot;acc:p52888] Subtracted 8651.4 9048.97 397.57
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Divided High confidence 3847.31 4409.22 1.14605
466 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted 2353.63 3225.65 872.02
neurolysin, mitochondrial precursor (ec 3.4.24.16) (neurotensin endopeptidase) (mitochondrial oligopeptidase m) (microsomal endopeptidase) (mep). [swissprot;acc:q9byt8] Low confidence 8651.4 9048.97 397.57
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided High confidence 3847.31 4409.22 1.14605
yippee-like protein 2 (digeorge syndrome-related protein fksg4). [swissprot;acc:q96qa6] Low confidence 8941.56 9388.99 1.05004
467 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Subtracted High confidence 1926.69 1056.02 870.67
metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 4864.25 5573.62 1.14583
striatin 4 (zinedin). [swissprot;acc:q9nrl3] Subtracted Low confidence 7018.98 7416.34 397.36
yippee-like protein 3 (digeorge syndrome-related protein fksg5). [swissprot;acc:q9bsj4] Divided 8941.65 9389.09 1.05004
468 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] High confidence 4869.15 5578.02 1.14558
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Subtracted Low confidence 7151 7548.35 397.35
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] High confidence 11143.5 10276.3 867.2
yippee-like protein 5. [swissprot;acc:q96ns1] Divided Low confidence 8940.99 9388.34 1.05003
469 lim domains containing 1. [refseq;acc:nm_014240] 7702.99 8088.26 1.05002
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] High confidence 3831.17 4388.74 1.14554
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Subtracted Low confidence 7870.27 8267.28 397.01
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] High confidence 11143.5 10276.3 867.2
470 block of proliferation 1. [swissprot;acc:q14137] Divided 3796.24 4348.59 1.1455
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Subtracted Low confidence 7870.27 8267.28 397.01
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] High confidence 5367.04 6233.12 866.08
probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Divided Low confidence 7702.99 8088.26 1.05002
471 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] High confidence 9649.61 11053.5 1.14549
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] Subtracted 5980.15 6843.48 863.33
postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171] Low confidence 8683.9 9080.72 396.82
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 7702.99 8088.26 1.05002
472 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Subtracted High confidence 5246.01 6109.31 863.3
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 7155.19 7551.48 396.29
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Divided High confidence 9649.61 11053.5 1.14549
473 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Subtracted Low confidence 8686.89 9082.91 396.02
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Divided 8840.55 9282.64 1.05001
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Subtracted High confidence 5979.95 6842.78 862.83
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Divided 9649.61 11053.5 1.14549
474 aquaporin 5. [swissprot;acc:p55064] Low confidence 8840.55 9282.64 1.05001

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/