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 700 to 749 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
88 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted Divided 37.3005 48.4141 1.29795
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared 105482 64137.2 1.64463
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Ranked Subtracted 249.663 298.263 48.6
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured 16074 12888.4 3185.6
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared 98517.9 56927.2 41590.7
89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Measured Divided 2414.22 1698.12 1.4217
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Rooted Subtracted 40.3372 24.3043 16.0329
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Measured 16071.6 12886.8 3184.8
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked Divided 88.2482 110.265 1.24949
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 249.663 298.263 48.6
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Rooted Divided 37.3005 48.4141 1.29795
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 105473 64132.3 1.64462
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted 105500 64146.3 41353.7
90 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Rooted Divided 37.3005 48.4141 1.29795
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Squared Subtracted 105482 64136.9 41345.1
necdin. [swissprot;acc:q99608] Ranked Divided 88.2482 110.265 1.24949
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Measured 2414.77 1698.75 1.4215
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Subtracted 16071.6 12886.8 3184.8
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] Ranked 249.663 298.263 48.6
transcription factor jun-d. [swissprot;acc:p17535] Rooted 63.636 79.6225 15.9865
transforming protein n-ras. [swissprot;acc:p01111] Squared Divided 105469 64130.2 1.64461
91 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 37.3005 48.4141 1.29795
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Subtracted 40.2812 24.3678 15.9134
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked Divided 88.2482 110.265 1.24949
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Measured 2416.53 1700.8 1.42082
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 1.60615
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Subtracted 105482 64137.2 41344.8
transcription factor lbx1. [swissprot;acc:p52954] Ranked 249.663 298.263 48.6
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Measured 16070.4 12886 3184.4
92 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 4117.67 5801.04 1.40882
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Rooted Subtracted 40.2812 24.3679 15.9133
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked Divided 88.2482 110.265 1.24949
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 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

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/