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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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 measured expected final Hugo
Results: HTML CSV LaTeX Showing element 58 to 107 of 3206 in total
Rank
description
measured
expected
final
Hugo
58 "DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 0.0511645 0.124441 0.411154684 no value
59 DISKS LARGE-ASSOCIATED PROTEIN 3 (DAP-3) (SAP90/PSD-95-ASSOCIATED PROTEIN 3) (SAPAP3) (PSD-95/SAP90 BINDING PROTEIN 3) (FRAGMENT). [SWISSPROT;Acc:O95886] 0.28264 0.68743 0.41115459 DLGAP3
60 CELLULAR REPRESSOR OF E1A-STIMULATED GENES. [RefSeq;Acc:NM_003851] 0.312681 0.760495 0.411154577 CREG1
61 PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2] no value
62 CELLULAR REPRESSOR OF E1A-STIMULATED GENES 2. [RefSeq;Acc:NM_153836] 0.237385 0.577362 0.411154527 CREG2
63 MITOCHONDRIAL FERRITIN; FERRITIN HEAVY CHAIN-LIKE; FERRITIN H SUBUNIT. [RefSeq;Acc:NM_177478] 0.685868 1.66819 0.411145013 FTMT
64 FERRITIN HEAVY POLYPEPTIDE-LIKE 17. [SWISSPROT;Acc:Q9BXU8] 0.605547 1.4734 0.410986154 FTHL17
65 DNA POLYMERASE EPSILON P17 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 3) (CHROMATIN ACCESSIBILITY COMPLEX 17) (HUCHRAC17) (CHRAC-17). [SWISSPROT;Acc:Q9NRF9] 0.446035 1.09489 0.407378823 POLE3
66 SYNAPSIN I (BRAIN PROTEIN 4.1). [SWISSPROT;Acc:P17600] 0.132875 0.327175 0.406128219 SYN1
67 PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR (PEROXISMORE RECEPTOR 1) (PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR) (PTS1-BP) (PEROXIN-5) (PTS1 RECEPTOR). [SWISSPROT;Acc:P50542] 1.42729 3.51439 0.406127379 PEX5
68 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 1 (HAIRY AND ENHANCER OF SPLIT RELATED-1) (HESR-1) (CARDIOVASCULAR HELIX-LOOP-HELIX FACTOR 2) (HES-RELATED REPRESSOR PROTEIN 2 HERP2). [SWISSPROT;Acc:Q9Y5J3] 0.0646859 0.159275 0.406127139 HEY1
69 SYNAPSIN II. [SWISSPROT;Acc:Q92777] 0.159227 0.392062 0.406127092 SYN2
70 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF-LIKE. [RefSeq;Acc:NM_014571] 0.0617004 0.151924 0.406126748 HEYL
71 ACTIN BINDING LIM PROTEIN 2. [RefSeq;Acc:NM_032432] 0.0620387 0.152757 0.406126724 ABLIM2
72 "DELTA3,5-DELTA2,4-DIENOYL-COA ISOMERASE, MITOCHONDRIAL PRECURSOR (EC 5.3.3.-). [SWISSPROT;Acc:Q13011]" 0.31296 0.770597 0.406126678 ECH1
73 TRANSCRIPTION FACTOR HES-1 (HAIRY AND ENHANCER OF SPLIT 1) (HAIRY- LIKE) (HHL) (HAIRY HOMOLOG). [SWISSPROT;Acc:Q14469] 0.285613 0.703261 0.406126602 HES1
74 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 2; GRIDLOCK; HES-RELATED REPRESSOR PROTEIN 1. [RefSeq;Acc:NM_012259] 0.0796134 0.196031 0.406126582 HEY2
75 MITOCHONDRIAL RIBOSOME RECYCLING FACTOR. [RefSeq;Acc:NM_138777] 0.291345 0.717375 0.406126503 MRRF
76 0.212647 0.523598 0.406126456 C22orf9
77 0.0637106 0.156874 0.406125935 ABLIM3
78 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 0.06383 0.157168 0.406125929 no value
79 SYNAPSIN III. [SWISSPROT;Acc:O14994] 0.133193 0.32796 0.406125747 SYN3
80 ACTIN-BINDING LIM PROTEIN 1 ISOFORM A; LIM ACTIN-BINDING PROTEIN 1; LIMATIN; ACTIN-BINDING LIM PROTEIN. [RefSeq;Acc:NM_002313] 0.0763094 0.187896 0.406125729 ABLIM1
81 TRANSCRIPTION FACTOR DP-2 (E2F DIMERIZATION PARTNER 2). [SWISSPROT;Acc:Q14188] 0.745698 1.87445 0.397822295 TFDP2
82 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] 0.198685 0.505165 0.393307137 E2F1
83 TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 0.204365 0.519607 0.393306865 E2F2
84 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). [SWISSPROT;Acc:P55010] 0.375556 0.956345 0.392699287 EIF5
85 TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 0.788778 2.02915 0.388723357 no value
86 RGS19-INTERACTING PROTEIN 1 (GAIP C-TERMINUS INTERACTING PROTEIN GIPC) (RGS-GAIP INTERACTING PROTEIN) (TAX INTERACTION PROTEIN 2) (TIP-2). [SWISSPROT;Acc:O14908] 1.20591 3.1266 0.385693725 GIPC1
87 0.113929 0.295729 0.38524798 PLEKHG6
88 APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796] 0.117195 0.30421 0.385243746 SHROOM2
89 0.152828 0.396725 0.385224022 no value
90 SHROOM-RELATED PROTEIN; F-ACTIN-BINDING PROTEIN; LIKELY ORTHOLOG OF MOUSE SHROOM. [RefSeq;Acc:NM_020859] SHROOM3
91 SHROOM4
92 0.914796 2.37847 0.38461532 no value
93 SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [SWISSPROT;Acc:Q13191] 0.502064 1.32571 0.378713293 CBLB
94 CBL E3 UBIQUITIN PROTEIN LIGASE (EC 6.3.2.-) (SIGNAL TRANSDUCTION PROTEIN CBL) (PROTO-ONCOGENE C-CBL). [SWISSPROT;Acc:P22681] 0.394562 1.04353 0.378103169 CBL
95 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 (POTASSIUM CHANNEL KV1.2) (RBK2) (HBK5) (NGK1) (MK2) (HUKIV). [SWISSPROT;Acc:P16389] 0.22158 0.589242 0.376042441 KCNA2
96 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 1 (POTASSIUM CHANNEL KV1.1) (HUKI) (HBK1). [SWISSPROT;Acc:Q09470] 0.185899 0.494524 0.375915021 KCNA1
97 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 4 (POTASSIUM CHANNEL KV1.4) (HK1) (HPCN2) (HBK4) (HUKII). [SWISSPROT;Acc:P22459] 0.166283 0.442453 0.375820709 KCNA4
98 VAV PROTO-ONCOGENE. [SWISSPROT;Acc:P15498] 0.379284 1.01082 0.375224076 VAV1
99 VAV-3 PROTEIN. [SWISSPROT;Acc:Q9UKW4] 0.380273 1.015 0.374653202 VAV3
100 "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE 1 ISOFORM B; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE I, 107KD; 4-PHOSPHATASE I; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE I. [RefSeq;Acc:NM_001566]" 0.0619579 0.165754 0.373794298 INPP4A
101 "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE II, 105KD; INOSITOL POLYPHOSPHATE 4-PHOSPHATASE II; 4-PHOSPHATASE II. [RefSeq;Acc:NM_003866]" 0.046965 0.125644 0.373794212 INPP4B
102 "SELENIDE,WATER DIKINASE 1 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 1) (SELENIUM DONOR PROTEIN 1). [SWISSPROT;Acc:P49903]" 0.0620748 0.166067 0.37379371 SEPHS1
103 "SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" 0.0447647 0.119758 0.373792983 SEPHS2
104 FLAVOPROTEIN OXIDOREDUCTASE MICAL2. [RefSeq;Acc:NM_014632] 0.42874 1.147 0.373792502 MICAL2
105 VAV-2 PROTEIN. [SWISSPROT;Acc:P52735] 0.433722 1.16696 0.371668266 VAV2
106 WISKOTT-ALDRICH SYNDROME PROTEIN INTERACTING PROTEIN (WASP INTERACTING PROTEIN) (PRPL-2 PROTEIN). [SWISSPROT;Acc:O43516] 0.23886 0.649898 0.367534598 WIPF1
107 SEQUESTOSOME 1; UBIQUITIN-BINDING PROTEIN P62; PHOSPHOTYROSINE INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN P62. [RefSeq;Acc:NM_003900] 0.0692099 0.188735 0.366704109 SQSTM1

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/