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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 351 to 400 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
88 KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 2411.93 1695.45 1.42259
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 48.4141 1.29795
89 CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Measured 2414.22 1698.12 1.4217
HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 105473 64132.3 1.64462
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked 88.2482 110.265 1.24949
SKP1A 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 37.3005 48.4141 1.29795
90 no value transforming protein n-ras. [swissprot;acc:p01111] Squared 105469 64130.2 1.64461
FBXW7 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 37.3005 48.4141 1.29795
KCND3 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
NDN necdin. [swissprot;acc:q99608] Ranked 88.2482 110.265 1.24949
91 CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 37.3005 48.4141 1.29795
KCND1 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
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked 88.2482 110.265 1.24949
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 1.60615
92 MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 88.2482 110.265 1.24949
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured 4117.67 5801.04 1.40882
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 29570.7 18601.8 1.58967
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted 37.3005 48.4141 1.29795
93 no value 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
ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Squared 29567 18601.6 1.58949
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted 37.3005 48.4141 1.29795
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Ranked 88.2482 110.265 1.24949
94 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 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
RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted 47.6504 36.9304 1.29028
RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared 84857.8 53402.4 1.58903
95 MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 88.2482 110.265 1.24949
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared 256169 162517 1.57626
RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted 47.6504 36.9304 1.29028
SON 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
96 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Squared 7744.68 4959.41 1.56161
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured 4110.14 5694.99 1.3856
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 88.2482 110.265 1.24949
RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Rooted 47.6504 36.9304 1.29028
97 APBA1 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 2820.51 3897.1 1.3817
CPSF4 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 227160 146079 1.55505
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 88.2482 110.265 1.24949
RGS20 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
98 KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 146079 1.55505
LBX1 transcription factor lbx1. [swissprot;acc:p52954] Rooted 47.6504 36.9304 1.29028
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 88.2482 110.265 1.24949
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured 2353.63 3225.65 1.3705
99 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 88.2482 110.265 1.24949
GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
SKP1A 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] Measured 2353.63 3225.65 1.3705
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared 226186 145568 1.55382
100 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
FBXW7 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] Measured 2353.63 3225.65 1.3705
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 110.265 1.24949
RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 36.9304 1.29028

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
- Hugo is the HGNC identifier if it exists
- 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/