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 Value Type description Interaction Map Network Comparison Type Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 725 to 774 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
network_comparison
green
91 Squared ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Divided 90432.9 1.60615 56304.2
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Subtracted 105482 41344.8 64137.2
Rooted cullin homolog 2 (cul-2). [swissprot;acc:q13617] Divided 37.3005 1.29795 48.4141
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Subtracted 40.2812 15.9134 24.3678
92 Measured dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 4117.67 1.40882 5801.04
transforming protein n-ras. [swissprot;acc:p01111] Subtracted 16069.8 3184.2 12885.6
Ranked melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 88.2482 1.24949 110.265
mosaic protein lgn. [swissprot;acc:p81274] Subtracted 249.663 48.6 298.263
Squared metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 29570.7 1.58967 18601.8
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Subtracted 105473 41340.7 64132.3
Rooted guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 40.2812 15.9133 24.3679
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided 37.3005 1.29795 48.4141
93 Measured formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 4245.52 1.39977 5942.75
sedlin. [swissprot;acc:o14582] Subtracted 17396.9 3087 20483.9
Ranked melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 88.2482 1.24949 110.265
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Subtracted 249.663 48.6 298.263
Squared beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided 29567 1.58949 18601.6
transforming protein n-ras. [swissprot;acc:p01111] Subtracted 105469 41338.8 64130.2
Rooted cullin homolog 1 (cul-1). [swissprot;acc:q13616] Divided 37.3005 1.29795 48.4141
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Subtracted 40.2805 15.9115 24.369
94 Measured huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 4247.86 1.39879 5941.88
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 17396.9 3087 20483.9
Ranked guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 249.663 48.6 298.263
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 88.2482 1.24949 110.265
Squared protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Subtracted 124319 37470.8 86848.2
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 84857.8 1.58903 53402.4
Rooted chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 47.6504 1.29028 36.9304
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Subtracted 40.2805 15.9114 24.3691
95 Measured bet3 homolog. [swissprot;acc:o43617] 17396.9 3087 20483.9
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Divided 2397.19 1.39481 3343.62
Ranked melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 88.2482 1.24949 110.265
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Subtracted 249.663 48.6 298.263
Squared protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided 256169 1.57626 162517
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted 123324 37046.1 86277.9
Rooted guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 40.2804 15.9112 24.3692
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided 47.6504 1.29028 36.9304
96 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 4110.14 1.3856 5694.99
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 16177.9 3057.5 19235.4
Ranked cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 48.278 153.671
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 88.2482 1.24949 110.265
Squared atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 7744.68 1.56161 4959.41
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 90226 36713 126939
Rooted guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 40.28 15.91 24.37
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 47.6504 1.29028 36.9304
97 Measured amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 2820.51 1.3817 3897.1
septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted 16067.4 3027 19094.4
Ranked amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 271.752 46.072 225.68
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 88.2482 1.24949 110.265
Squared 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] 227160 1.55505 146079
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 126408 36467.5 89940.5

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/