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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
76 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 20446.1 24136.4 3690.3
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] Divided 4599.26 3058.57 1.50373
77 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 20446.1 24136.4 3690.3
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] Divided 4612.39 3093.6 1.49095
78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 20446.1 24136.4 3690.3
79 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 3074.57 4567.51 1.48558
80 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 20446.1 24136.4 3690.3
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 4133.47 5945.32 1.43834
81 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 20446.1 24136.4 3690.3
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided 4136.36 5943.56 1.43691
82 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted 20446.1 24136.4 3690.3
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 4172.91 5954.48 1.42694
83 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 21644.2 18098.7 3545.5
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided 4932.27 7033.29 1.42597
84 jun dimerization protein. [refseq;acc:nm_130469]
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Subtracted 21632.5 18090 3542.5
85 fos-related antigen 2. [swissprot;acc:p15408] Divided 4941.95 7037.11 1.42395
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 21370.8 17896.5 3474.3
86 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided 4942.49 7037.32 1.42384
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 21370.8 17896.5 3474.3
87 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided 4944.3 7038.04 1.42347
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted 20287.2 17083.8 3203.4
88 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 2411.93 1695.45 1.42259
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted 16074 12888.4 3185.6
89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 2414.22 1698.12 1.4217
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Subtracted 16071.6 12886.8 3184.8
90 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
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Subtracted 16071.6 12886.8 3184.8
91 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 2416.53 1700.8 1.42082
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Subtracted 16070.4 12886 3184.4
92 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 4117.67 5801.04 1.40882
transforming protein n-ras. [swissprot;acc:p01111] Subtracted 16069.8 12885.6 3184.2
93 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 4245.52 5942.75 1.39977
sedlin. [swissprot;acc:o14582] Subtracted 17396.9 20483.9 3087
94 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 4247.86 5941.88 1.39879
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 17396.9 20483.9 3087
95 bet3 homolog. [swissprot;acc:o43617]
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 2397.19 3343.62 1.39481
96 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 4110.14 5694.99 1.3856
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 16177.9 19235.4 3057.5
97 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] Divided 2820.51 3897.1 1.3817
septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted 16067.4 19094.4 3027
98 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 3008
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 2353.63 3225.65 1.3705
99 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]
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 15999.1 19007.1 3008
100 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] Divided 2353.63 3225.65 1.3705
septin 6. [swissprot;acc:q14141] Subtracted 15959.9 18957.1 2997.2

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/