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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Network Comparison Type Gene Rank Value Type Interaction Map description red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 101 to 150 of 25824 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
network_comparison
green
26 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1833.01 2.0534 892.67
Ranked pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 58 1.31818 44
Squared neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 143.692 3.18404 457.521
Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 40.3362 1.66024 24.2954
27 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 1834.33 2.04922 895.134
Ranked mitochondrial solute carrier protein. [refseq;acc:nm_145305] 58 1.31818 44
Squared neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 143.692 3.18404 457.521
Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 40.3364 1.66015 24.2968
28 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1834.36 2.04912 895.194
Ranked cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 1.31416 153.671
Squared neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 143.692 3.18404 457.521
Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 40.3372 1.65967 24.3043
29 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 1834.52 2.04858 895.507
Ranked uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 1.29991 243.678
Squared chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 143.692 3.18404 457.521
Rooted 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
30 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1834.59 2.04837 895.633
Ranked 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
Squared 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
Rooted microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 26.0288 1.65937 43.1914
31 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1834.63 2.04827 895.697
Ranked 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
Squared beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 9924.76 2.53372 25146.6
Rooted protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 26.0288 1.65937 43.1914
32 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 1834.73 2.04793 895.893
Ranked serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 187.462 1.29985 243.673
Squared beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 9924.76 2.53372 25146.6
Rooted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 26.0288 1.65937 43.1914
33 Measured guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1835.3 2.04611 896.972
Ranked 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] 188.688 1.28647 242.742
Squared spermatogenesis associated 6. [refseq;acc:nm_019073] 9924.76 2.53372 25146.6
Rooted protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 26.0288 1.65937 43.1914
34 Measured guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1836.71 2.02382 907.546
Ranked 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] 189.07 1.28235 242.453
Squared amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 9924.76 2.53372 25146.6
Rooted guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 40.2812 1.65305 24.3678
35 Measured guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1836.71 2.02378 907.564
Ranked nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 260.532 1.27519 204.309
Squared 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 106226 1.80879 192141
Rooted guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 40.2812 1.65304 24.3679
36 Measured guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 1836.76 2.02344 907.741
Ranked ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 260.532 1.27519 204.309
Squared pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 106226 1.80879 192141
Rooted guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 40.2805 1.65294 24.369
37 Measured guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 1836.76 2.02339 907.763
Ranked protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 322 1.27273 253
Squared pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 106226 1.80879 192141
Rooted guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 40.2805 1.65293 24.3691
38 Measured guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 1836.76 2.02337 907.774
Ranked microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 322 1.27273 253

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/