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 732 to 781 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
92 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared Divided 29570.7 18601.8 1.58967
mosaic protein lgn. [swissprot;acc:p81274] Ranked Subtracted 249.663 298.263 48.6
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted Divided 37.3005 48.4141 1.29795
transforming protein n-ras. [swissprot;acc:p01111] Measured Subtracted 16069.8 12885.6 3184.2
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 105473 64132.3 41340.7
93 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided 29567 18601.6 1.58949
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted 37.3005 48.4141 1.29795
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 4245.52 5942.75 1.39977
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Rooted Subtracted 40.2805 24.369 15.9115
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Ranked Divided 88.2482 110.265 1.24949
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Subtracted 249.663 298.263 48.6
sedlin. [swissprot;acc:o14582] Measured 17396.9 20483.9 3087
transforming protein n-ras. [swissprot;acc:p01111] Squared 105469 64130.2 41338.8
94 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted Divided 47.6504 36.9304 1.29028
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Ranked Subtracted 249.663 298.263 48.6
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Rooted 40.2805 24.3691 15.9114
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured Divided 4247.86 5941.88 1.39879
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked 88.2482 110.265 1.24949
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Squared Subtracted 124319 86848.2 37470.8
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 84857.8 53402.4 1.58903
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Measured Subtracted 17396.9 20483.9 3087
95 bet3 homolog. [swissprot;acc:o43617]
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Rooted 40.2804 24.3692 15.9112
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked Divided 88.2482 110.265 1.24949
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared 256169 162517 1.57626
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked Subtracted 249.663 298.263 48.6
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted Divided 47.6504 36.9304 1.29028
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] Measured 2397.19 3343.62 1.39481
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared Subtracted 123324 86277.9 37046.1
96 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided 7744.68 4959.41 1.56161
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked Subtracted 201.949 153.671 48.278
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Rooted 40.28 24.37 15.91
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Divided 4110.14 5694.99 1.3856
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 88.2482 110.265 1.24949
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Rooted 47.6504 36.9304 1.29028
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Subtracted 16177.9 19235.4 3057.5
Squared 90226 126939 36713
97 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] Measured Divided 2820.51 3897.1 1.3817
Ranked Subtracted 271.752 225.68 46.072
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] Squared Divided 227160 146079 1.55505
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 126408 89940.5 36467.5
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Rooted 40.2797 24.3705 15.9092
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked Divided 88.2482 110.265 1.24949
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Rooted 47.6504 36.9304 1.29028
septin 10 isoform 1. [refseq;acc:nm_144710] Measured Subtracted 16067.4 19094.4 3027
98 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 3008
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Rooted 40.2797 24.3705 15.9092
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked Divided 88.2482 110.265 1.24949
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured 2353.63 3225.65 1.3705
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked Subtracted 204.641 160.957 43.684

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/