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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 66312 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
Interaction Map
red
green
network_comparison
199 serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Measured Divided High confidence 4916.8 3888.18 1.26455
single-stranded dna-binding protein 4. [swissprot;acc:q9bwg4] Squared Subtracted Low confidence 52164.3 47095.3 5069
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Divided High confidence 61.2893 70.3856 1.14842
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 95488.6 1.34373
tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Rooted Low confidence 70.8512 75.1709 1.06097
200 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Ranked Subtracted High confidence 241.808 267.335 25.527
60s ribosomal protein l27. [swissprot;acc:p08526] Rooted Divided Low confidence 69.691 73.939 1.06095
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Ranked 219.543 208.868 1.05111
anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Subtracted 213.495 203.244 10.251
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured High confidence 10635.3 12111.4 1476.1
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Squared Divided Low confidence 54179.7 48910.9 1.10772
cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] Measured Subtracted 9810.95 10381.3 570.35
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided High confidence 4808.79 6074.21 1.26315
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 276.018 1.1372
gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 95488.6 1.34373
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Subtracted 42411.6 55802.1 13390.5
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Rooted Low confidence 69.9166 74.219 4.3024
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided High confidence 61.2893 70.3856 1.14842
rad50-interacting protein 1. [refseq;acc:nm_021930] Measured Low confidence 6926.74 7434.04 1.07324
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Rooted Subtracted High confidence 63.5827 53.0856 10.4971
tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] Squared Low confidence 52164 47095.1 5068.9
201 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked High confidence 241.828 267.346 25.518
a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured Divided Low confidence 10392.7 9683.56 1.07323
aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Subtracted 9249.74 9818.95 569.21
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared Divided High confidence 71033.4 95440.2 1.3436
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Rooted Subtracted 138.375 127.926 10.449
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked Divided Low confidence 208.591 219.23 1.051
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 71.1262 75.4476 1.06076
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] High confidence 61.2893 70.3856 1.14842
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Squared Low confidence 52176.8 47103.2 1.10771
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] Subtracted High confidence 42411.6 55802.1 13390.5
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted Low confidence 70.4583 74.7299 4.2716
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Divided High confidence 240.133 211.382 1.13601
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured 4810.22 6075.04 1.26294
tenascin n precursor (fragment). [sptrembl;acc:q9uqp3] Squared Subtracted Low confidence 52163.9 47095 5068.9
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured High confidence 10603.5 12069.5 1466
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Ranked Low confidence 203.935 214.089 10.154
202 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted Divided 71.0652 75.377 1.06067
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked Subtracted High confidence 240.758 266.079 25.321
aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Measured Low confidence 9246.23 9814.59 568.36
calsyntenin-1 precursor. [swissprot;acc:o94985] High confidence 10603.5 12069.5 1466
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Divided 71030.1 95434.8 1.34358
dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Ranked Subtracted Low confidence 178.507 168.371 10.136
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured Divided High confidence 4812.01 6076.09 1.26269
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked Low confidence 211.51 222.252 1.05079
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Subtracted High confidence 42411.6 55802.1 13390.5
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Divided Low confidence 55537.3 50139.7 1.10765
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 10391.8 9682.99 1.0732
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Ranked High confidence 201.478 228.784 1.13553
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Subtracted Low confidence 71.0886 75.3451 4.2565

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/