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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Gene Rank description Value Type Network Comparison Type red Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 201 to 250 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
network_comparison
green
26 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Rooted Divided 40.3362 1.66024 24.2954
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 1833.01 2.0534 892.67
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 23693.7 5430.7 18263
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 219048 89286 129762
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted 146.94 20.106 167.046
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Squared Divided 143.692 3.18404 457.521
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Ranked 58 1.31818 44
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 322 69 253
27 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Measured Divided 1834.33 2.04922 895.134
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Rooted 40.3364 1.66015 24.2968
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked Subtracted 267.136 68.941 336.077
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared 219048 89286 129762
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 23693.7 5430.7 18263
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked Divided 58 1.31818 44
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Rooted Subtracted 146.94 20.106 167.046
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared Divided 143.692 3.18404 457.521
28 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked 201.949 1.31416 153.671
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted Subtracted 149.165 19.466 129.699
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 40.3372 1.65967 24.3043
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 1834.36 2.04912 895.194
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked Subtracted 267.136 68.941 336.077
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 219048 89286 129762
necdin. [swissprot;acc:q99608] Measured 23693.7 5430.7 18263
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared Divided 143.692 3.18404 457.521
29 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured 1834.52 2.04858 895.507
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked Subtracted 267.139 68.936 336.075
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 23693.7 5430.7 18263
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Squared 219048 89286 129762
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted Divided 26.0288 1.65937 43.1914
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 210.928 18.763 192.165
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked Divided 187.458 1.29991 243.678
30 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted Subtracted 60.8022 18.7077 79.5099
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Squared Divided 143.692 3.18404 457.521
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Measured 1834.59 2.04837 895.633
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Subtracted 267.14 68.935 336.075
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 23693.7 5430.7 18263
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted Divided 26.0288 1.65937 43.1914
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Ranked 187.457 1.29991 243.678
trophinin. [swissprot;acc:q12816] Squared Subtracted 219048 89286 129762
31 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 106226 85915 192141
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided 9924.76 2.53372 25146.6
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured 1834.63 2.04827 895.697
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked Subtracted 267.14 68.935 336.075
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Measured 23693.7 5430.7 18263
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted 40.0958 18.7028 58.7986
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Divided 26.0288 1.65937 43.1914
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Ranked 187.458 1.2999 243.677
32 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared 9924.76 2.53372 25146.6
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Rooted 26.0288 1.65937 43.1914

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/