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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 301 to 350 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
76 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Subtracted 0 598 184 414
dead-box protein. [refseq;acc:nm_018665] Divided 313.667 183 1.71403
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 1 20446.1 24136.4 3690.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Divided 4599.26 3058.57 1.50373
77 heat shock factor binding protein 1. [swissprot;acc:o75506] Subtracted 0 1631.18 1233.41 397.77
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1 20446.1 24136.4 3690.3
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Divided 0 712.071 416.524 1.70956
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 1 4612.39 3093.6 1.49095
78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 20446.1 24136.4 3690.3
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Divided 0 161 95 1.69474
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Subtracted 1251.66 858.525 393.135
79 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 2464 2076.5 387.5
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 1 20446.1 24136.4 3690.3
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Divided 0 323.79 544.991 1.68316
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 3074.57 4567.51 1.48558
80 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 20446.1 24136.4 3690.3
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 4133.47 5945.32 1.43834
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 293 493 1.68259
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Subtracted 2464 2076.5 387.5
81 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 1 20446.1 24136.4 3690.3
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided 4136.36 5943.56 1.43691
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Subtracted 0 2715.75 3103.01 387.26
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Divided 30 50 1.66667
82 importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 191.333 115.333 1.65896
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted 1 20446.1 24136.4 3690.3
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 4172.91 5954.48 1.42694
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Subtracted 0 8243.06 8627.63 384.57
83 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Divided 166.114 100.887 1.64654
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Subtracted 4159.87 3775.43 384.44
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 1 21644.2 18098.7 3545.5
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided 4932.27 7033.29 1.42597
84 jun dimerization protein. [refseq;acc:nm_130469]
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 0 973.698 1601.52 1.64478
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 3336.48 2957.12 379.36
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 1 21632.5 18090 3542.5
85 fos-related antigen 2. [swissprot;acc:p15408] Divided 4941.95 7037.11 1.42395
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Subtracted 0 266 645 379
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Divided 679.449 1106.88 1.62908
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 1 21370.8 17896.5 3474.3
86 alpha crystallin a chain. [swissprot;acc:p02489] Divided 0 55.3059 89.2447 1.61366
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 4942.49 7037.32 1.42384
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 21370.8 17896.5 3474.3
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 0 1526.38 1150.51 375.87
87 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided 1 4944.3 7038.04 1.42347
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Subtracted 0 1283.48 1649.37 365.89
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 1 20287.2 17083.8 3203.4
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Divided 0 304.664 483.809 1.58801
88 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 364 0 364
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 1 2411.93 1695.45 1.42259

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/