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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 325 to 374 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
82 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted High confidence 252.329 202.004 50.325
DGKH diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Divided Low confidence 226.981 208.077 1.09085
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 267.636 335.359 1.25304
TAF2 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] Subtracted Low confidence 237.567 219.229 18.338
83 DGKD diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Divided 226.981 208.077 1.09085
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Subtracted High confidence 252.309 201.998 50.311
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 88.2482 110.265 1.24949
STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Subtracted Low confidence 228.743 210.764 17.979
84 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Divided 226.338 207.874 1.08882
HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Subtracted High confidence 252.296 201.995 50.301
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Divided 88.2482 110.265 1.24949
OPHN1 oligophrenin 1. [swissprot;acc:o60890] Subtracted Low confidence 233.837 215.973 17.864
85 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided High confidence 88.2482 110.265 1.24949
ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Subtracted Low confidence 233.592 215.846 17.746
KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 225.735 245.308 1.08671
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted High confidence 296.677 247.559 49.118
86 DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Divided Low confidence 233.922 215.309 1.08645
DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Subtracted High confidence 335 286 49
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Divided 88.2482 110.265 1.24949
ROGDI leucine zipper domain protein. [refseq;acc:nm_024589] Subtracted Low confidence 221.996 238.82 16.824
87 DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] 229.556 213.456 16.1
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] Divided 225.545 244.933 1.08596
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence 88.2482 110.265 1.24949
RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Subtracted 249.663 298.263 48.6
88 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Divided 88.2482 110.265 1.24949
CPD carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Subtracted Low confidence 16 32 16
KCND1 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
RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Subtracted High confidence 249.663 298.263 48.6
89 MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided 88.2482 110.265 1.24949
RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 249.663 298.263 48.6
STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Divided Low confidence 228.743 210.764 1.0853
UBR4 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Subtracted 165.535 149.799 15.736
90 NDN necdin. [swissprot;acc:q99608] Divided High confidence 88.2482 110.265 1.24949
NEURL neuralized-like. [refseq;acc:nm_004210] Subtracted Low confidence 232.704 216.996 15.708
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] High confidence 249.663 298.263 48.6
TAF2 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
91 FAM89B mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Subtracted 227.429 211.97 15.459
LBX1 transcription factor lbx1. [swissprot;acc:p52954] High confidence 249.663 298.263 48.6
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided 88.2482 110.265 1.24949
OPHN1 oligophrenin 1. [swissprot;acc:o60890] Low confidence 233.837 215.973 1.08271
92 ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 233.592 215.846 1.08222
E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Subtracted 220.497 205.364 15.133
GPSM2 mosaic protein lgn. [swissprot;acc:p81274] High confidence 249.663 298.263 48.6
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 88.2482 110.265 1.24949
93 DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Low confidence 247.334 228.84 1.08082
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Subtracted 220.497 205.364 15.133
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided High confidence 88.2482 110.265 1.24949
RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Subtracted 249.663 298.263 48.6
94 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 88.2482 110.265 1.24949
ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Subtracted Low confidence 219.277 204.212 15.065

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/