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 Value Type Network Comparison Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 201 to 250 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Network Comparison Type
description
red
network_comparison
green
26 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1833.01 2.0534 892.67
Subtracted hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 23693.7 5430.7 18263
Ranked Divided pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 58 1.31818 44
Subtracted protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 322 69 253
Squared Divided neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 143.692 3.18404 457.521
Subtracted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 219048 89286 129762
Rooted Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 40.3362 1.66024 24.2954
Subtracted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 146.94 20.106 167.046
27 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 1834.33 2.04922 895.134
Subtracted melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 23693.7 5430.7 18263
Ranked Divided mitochondrial solute carrier protein. [refseq;acc:nm_145305] 58 1.31818 44
Subtracted guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 68.941 336.077
Squared Divided neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 143.692 3.18404 457.521
Subtracted melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 219048 89286 129762
Rooted Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 40.3364 1.66015 24.2968
Subtracted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 146.94 20.106 167.046
28 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1834.36 2.04912 895.194
Subtracted necdin. [swissprot;acc:q99608] 23693.7 5430.7 18263
Ranked Divided cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 1.31416 153.671
Subtracted guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 68.941 336.077
Squared Divided neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 143.692 3.18404 457.521
Subtracted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 219048 89286 129762
Rooted Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 40.3372 1.65967 24.3043
Subtracted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 149.165 19.466 129.699
29 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 1834.52 2.04858 895.507
Subtracted melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 23693.7 5430.7 18263
Ranked Divided uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 1.29991 243.678
Subtracted guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 267.139 68.936 336.075
Squared Divided chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 143.692 3.18404 457.521
Subtracted 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] 219048 89286 129762
Rooted Divided protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 26.0288 1.65937 43.1914
Subtracted putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 210.928 18.763 192.165
30 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1834.59 2.04837 895.633
Subtracted melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 23693.7 5430.7 18263
Ranked Divided 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] 187.457 1.29991 243.678
Subtracted guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 267.14 68.935 336.075
Squared Divided 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] 143.692 3.18404 457.521
Subtracted trophinin. [swissprot;acc:q12816] 219048 89286 129762
Rooted Divided microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 26.0288 1.65937 43.1914
Subtracted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 60.8022 18.7077 79.5099
31 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1834.63 2.04827 895.697
Subtracted melanoma antigen, family b, 6. [refseq;acc:nm_173523] 23693.7 5430.7 18263
Ranked Divided 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] 187.458 1.2999 243.677
Subtracted guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14 68.935 336.075
Squared Divided beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 9924.76 2.53372 25146.6
Subtracted 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 106226 85915 192141
Rooted Divided protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 26.0288 1.65937 43.1914
Subtracted protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 40.0958 18.7028 58.7986
32 Measured Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 1834.73 2.04793 895.893
Subtracted melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 23693.7 5430.7 18263

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/