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 description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 475 to 524 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
60 Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Subtracted 269.254 327.655 58.401
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Divided 266.864 336.184 1.25976
Squared melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 219048 129762 1.68808
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 192904 126167 66737
Rooted melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 137.446 120.823 16.623
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] Divided 35.6294 49.8119 1.39806
61 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Subtracted 6475.5 10307.5 3832
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 4489.19 2765.82 1.6231
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 266.864 336.182 1.25975
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] Subtracted 269.248 327.642 58.394
Squared necdin. [swissprot;acc:q99608] Divided 219048 129762 1.68808
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Subtracted 192779 126095 66684
Rooted kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 43.4291 31.7159 1.36932
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 137.446 120.823 16.623
62 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 3832
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 4489.19 2765.82 1.6231
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 266.865 336.181 1.25974
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 269.23 327.601 58.371
Squared melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided 219048 129762 1.68808
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 189976 124480 65496
Rooted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 137.446 120.823 16.623
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 43.4519 31.7522 1.36847
63 Measured myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 2765.82 1.6231
spermatogenesis associated 6. [refseq;acc:nm_019073] Subtracted 6475.5 10307.5 3832
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 266.865 336.178 1.25973
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] Subtracted 260.532 204.309 56.223
Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 219048 129762 1.68808
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 189976 124480 65496
Rooted kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Divided 43.4554 31.7576 1.36835
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 137.446 120.823 16.623
64 Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 10307.5 3832
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 4489.19 2765.82 1.6231
Ranked 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] Subtracted 260.532 204.309 56.223
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 266.868 336.159 1.25965
Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 144940 81169.7 63770.3
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 219048 129762 1.68808
Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 63.8686 47.2654 1.35128
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 137.446 120.823 16.623
65 Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 22515.5 18702.6 3812.9
neuralized-like. [refseq;acc:nm_004210] Divided 1657.68 2690.25 1.6229
Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 336.077 1.25807
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Subtracted 187.457 243.678 56.221
Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 219048 129762 1.68808
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted 144912 81155 63757
Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 63.8686 47.2654 1.35128
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted 137.446 120.823 16.623
66 Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 14008 3749.5
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Divided 1991.03 3221.38 1.61795
Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 336.077 1.25807
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Subtracted 187.458 243.678 56.22

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/