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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1391 to 1440 of 66312 in total
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
Interaction Map
red
green
network_comparison
87 SHOC2 Squared leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Divided High confidence 105482 64136.9 1.64464
SLC7A6 Rooted solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Subtracted Low confidence 68.7629 75.4877 6.7248
88 no value Ranked hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Divided High confidence 88.2482 110.265 1.24949
Squared ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 105482 64137.2 1.64463
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 98517.9 56927.2 41590.7
Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 40.3364 24.2968 16.0396
ATG3 Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided Low confidence 60759.9 50515.5 1.2028
BACH2 Rooted transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] 79.2778 86.7076 1.09372
CPD Ranked carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Subtracted 16 32 16
EIF4B Rooted eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] 68.7629 75.4877 6.7248
HAAO Squared 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 65044.3 74962.3 9918
KCND1 Ranked potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 225.428 244.701 1.0855
KCND2 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 2411.93 1695.45 1.42259
KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted 16074 12888.4 3185.6
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Low confidence 11285.3 10318.5 966.8
MAK serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Divided 9631.47 10633 1.10399
PSEN2 Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] High confidence 37.3005 48.4141 1.29795
RGS19 Ranked regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Subtracted 249.663 298.263 48.6
89 BEST1 Rooted bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] Divided Low confidence 187.345 204.579 1.09199
CTH Measured cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence 2414.22 1698.12 1.4217
GNG11 Rooted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 40.3372 24.3043 16.0329
HRAS Squared transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Divided 105473 64132.3 1.64462
ICK Measured intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Low confidence 9623.55 10621.3 1.10368
KRAS Squared transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted High confidence 105500 64146.3 41353.7
MAGEA4 Measured melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Low confidence 11285.3 10318.5 966.8
MAGEA6 Ranked melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided High confidence 88.2482 110.265 1.24949
OTC Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Subtracted Low confidence 65896.9 75670.5 9773.6
PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 69693.1 58164.5 1.19821
RBM15 Ranked putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted High confidence 249.663 298.263 48.6
SHOC2 Measured leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 16071.6 12886.8 3184.8
SKP1A Rooted 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] Divided 37.3005 48.4141 1.29795
SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Subtracted Low confidence 68.7629 75.4877 6.7248
STARD7 Ranked star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Divided 228.743 210.764 1.0853
UBR4 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Subtracted 165.535 149.799 15.736
90 no value Measured melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 11285.3 10318.5 966.8
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] High confidence 16071.6 12886.8 3184.8
Squared transforming protein n-ras. [swissprot;acc:p01111] Divided 105469 64130.2 1.64461
BEST4 Rooted vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Low confidence 187.325 204.557 1.09199
BRAP Squared brca1 associated protein. [refseq;acc:nm_006768] 83524.5 69821.2 1.19626
FBXW7 Rooted 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] High confidence 37.3005 48.4141 1.29795
JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 63.636 79.6225 15.9865
KCND3 Measured 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] Divided 2414.77 1698.75 1.4215
NDN Ranked necdin. [swissprot;acc:q99608] 88.2482 110.265 1.24949
NEURL neuralized-like. [refseq;acc:nm_004210] Subtracted Low confidence 232.704 216.996 15.708
PHB Squared prohibitin. [swissprot;acc:p35232] 73503.9 82930.5 9426.6
RGS20 Ranked 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] High confidence 249.663 298.263 48.6
SEPT8 Rooted septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 98.7481 105.459 6.7109
SHOC2 Squared leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] High confidence 105482 64136.9 41345.1
TAF2 Ranked tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Divided Low confidence 237.567 219.229 1.08365
VASP Measured vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] 12768 11571.4 1.10341

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/