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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 328 to 377 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
82 Rooted ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 60.8022 79.5099 1.30768
83 Measured FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 4932.27 7033.29 1.42597
Ranked MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 110.265 1.24949
Squared PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 117718 70505.9 1.66962
Rooted PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 63.6507 48.7127 1.30666
84 Measured no value jun dimerization protein. [refseq;acc:nm_130469] 4932.27 7033.29 1.42597
Ranked MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 88.2482 110.265 1.24949
Squared BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 117515 70412.3 1.66896
Rooted NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 46.7419 60.9337 1.30362
85 Measured FOSL2 fos-related antigen 2. [swissprot;acc:p15408] 4941.95 7037.11 1.42395
Ranked no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 88.2482 110.265 1.24949
Squared ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 67438.6 40697 1.65709
Rooted NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 46.7419 60.9337 1.30362
86 Measured FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 4942.49 7037.32 1.42384
Ranked MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 110.265 1.24949
Squared KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 105500 64146.3 1.64468
Rooted PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 63.6205 48.8838 1.30146
87 Measured FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 4944.3 7038.04 1.42347
Ranked MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 88.2482 110.265 1.24949
Squared SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 105482 64136.9 1.64464
Rooted 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] 42.2825 54.9687 1.30003
88 Measured KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 2411.93 1695.45 1.42259
Ranked no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 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
Rooted PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 37.3005 48.4141 1.29795
89 Measured CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 2414.22 1698.12 1.4217
Ranked MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 88.2482 110.265 1.24949
Squared HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 105473 64132.3 1.64462
Rooted 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] 37.3005 48.4141 1.29795
90 Measured 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] 2414.77 1698.75 1.4215
Ranked NDN necdin. [swissprot;acc:q99608] 88.2482 110.265 1.24949
Squared no value transforming protein n-ras. [swissprot;acc:p01111] 105469 64130.2 1.64461
Rooted 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] 37.3005 48.4141 1.29795
91 Measured KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 2416.53 1700.8 1.42082
Ranked MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 88.2482 110.265 1.24949
Squared RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 90432.9 56304.2 1.60615
Rooted CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 37.3005 48.4141 1.29795
92 Measured NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 4117.67 5801.04 1.40882
Ranked MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 88.2482 110.265 1.24949
Squared PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 29570.7 18601.8 1.58967
Rooted PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 37.3005 48.4141 1.29795
93 Measured no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 4245.52 5942.75 1.39977
Ranked MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] 88.2482 110.265 1.24949
Squared ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 29567 18601.6 1.58949
Rooted CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 37.3005 48.4141 1.29795
94 Measured no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 4247.86 5941.88 1.39879
Ranked melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 88.2482 110.265 1.24949
Squared RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 84857.8 53402.4 1.58903
Rooted RBM15B chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 47.6504 36.9304 1.29028
95 Measured 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] 2397.19 3343.62 1.39481

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/