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.


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Rank Gene expected description final measured Hugo
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
Rank
expected
description
final
measured
Hugo
51 0.159562 LIMKAIN B1. [RefSeq;Acc:NM_019081] 0.411156165 0.0656049 KIAA0430
52 1.42639 KININOGEN PRECURSOR (ALPHA-2-THIOL PROTEINASE INHIBITOR) [CONTAINS: BRADYKININ]. [SWISSPROT;Acc:P01042] 0.411156135 0.586469 KNG1
53 0.775495 DISKS LARGE-ASSOCIATED PROTEIN 2 (DAP-2) (SAP90/PSD-95-ASSOCIATED PROTEIN 2) (SAPAP2) (PSD-95/SAP90 BINDING PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q9P1A6] 0.411155456 0.318849 no value
54 0.629835 PUTATIVE ADENOSYLHOMOCYSTEINASE 2 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:O43865] 0.411155303 0.25896 AHCYL1
55 0.562729 0.411155281 0.231369 no value
56 0.920789 DISKS LARGE-ASSOCIATED PROTEIN 1 (DAP-1) (GUANYLATE KINASE-ASSOCIATED PROTEIN) (HGKAP) (SAP90/PSD-95-ASSOCIATED PROTEIN 1) (SAPAP1) (PSD- 95/SAP90 BINDING PROTEIN 1). [SWISSPROT;Acc:O14490] 0.411154999 0.378587 DLGAP1
57 DISKS LARGE-ASSOCIATED PROTEIN 4 (DAP-4) (SAP90/PSD-95-ASSOCIATED PROTEIN 4) (SAPAP4) (PSD-95/SAP90 BINDING PROTEIN 4). [SWISSPROT;Acc:Q9Y2H0] DLGAP4
58 0.124441 "DJ681N20.2 (NOVEL PROTEIN SIMILAR TO FERRITIN, LIGHT POLYPEPTIDE (FTL)). [SPTREMBL;Acc:Q9BYW6]" 0.411154684 0.0511645 no value
59 0.68743 DISKS LARGE-ASSOCIATED PROTEIN 3 (DAP-3) (SAP90/PSD-95-ASSOCIATED PROTEIN 3) (SAPAP3) (PSD-95/SAP90 BINDING PROTEIN 3) (FRAGMENT). [SWISSPROT;Acc:O95886] 0.41115459 0.28264 DLGAP3
60 0.760495 CELLULAR REPRESSOR OF E1A-STIMULATED GENES. [RefSeq;Acc:NM_003851] 0.411154577 0.312681 CREG1
61 PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2] no value
62 0.577362 CELLULAR REPRESSOR OF E1A-STIMULATED GENES 2. [RefSeq;Acc:NM_153836] 0.411154527 0.237385 CREG2
63 1.66819 MITOCHONDRIAL FERRITIN; FERRITIN HEAVY CHAIN-LIKE; FERRITIN H SUBUNIT. [RefSeq;Acc:NM_177478] 0.411145013 0.685868 FTMT
64 1.4734 FERRITIN HEAVY POLYPEPTIDE-LIKE 17. [SWISSPROT;Acc:Q9BXU8] 0.410986154 0.605547 FTHL17
65 1.09489 DNA POLYMERASE EPSILON P17 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 3) (CHROMATIN ACCESSIBILITY COMPLEX 17) (HUCHRAC17) (CHRAC-17). [SWISSPROT;Acc:Q9NRF9] 0.407378823 0.446035 POLE3
66 0.327175 SYNAPSIN I (BRAIN PROTEIN 4.1). [SWISSPROT;Acc:P17600] 0.406128219 0.132875 SYN1
67 3.51439 PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR (PEROXISMORE RECEPTOR 1) (PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR) (PTS1-BP) (PEROXIN-5) (PTS1 RECEPTOR). [SWISSPROT;Acc:P50542] 0.406127379 1.42729 PEX5
68 0.159275 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] 0.406127139 0.0646859 HEY1
69 0.392062 SYNAPSIN II. [SWISSPROT;Acc:Q92777] 0.406127092 0.159227 SYN2
70 0.151924 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF-LIKE. [RefSeq;Acc:NM_014571] 0.406126748 0.0617004 HEYL
71 0.152757 ACTIN BINDING LIM PROTEIN 2. [RefSeq;Acc:NM_032432] 0.406126724 0.0620387 ABLIM2
72 0.770597 "DELTA3,5-DELTA2,4-DIENOYL-COA ISOMERASE, MITOCHONDRIAL PRECURSOR (EC 5.3.3.-). [SWISSPROT;Acc:Q13011]" 0.406126678 0.31296 ECH1
73 0.703261 TRANSCRIPTION FACTOR HES-1 (HAIRY AND ENHANCER OF SPLIT 1) (HAIRY- LIKE) (HHL) (HAIRY HOMOLOG). [SWISSPROT;Acc:Q14469] 0.406126602 0.285613 HES1
74 0.196031 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 2; GRIDLOCK; HES-RELATED REPRESSOR PROTEIN 1. [RefSeq;Acc:NM_012259] 0.406126582 0.0796134 HEY2
75 0.717375 MITOCHONDRIAL RIBOSOME RECYCLING FACTOR. [RefSeq;Acc:NM_138777] 0.406126503 0.291345 MRRF
76 0.523598 0.406126456 0.212647 C22orf9
77 0.156874 0.406125935 0.0637106 ABLIM3
78 0.157168 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 0.406125929 0.06383 no value
79 0.32796 SYNAPSIN III. [SWISSPROT;Acc:O14994] 0.406125747 0.133193 SYN3
80 0.187896 ACTIN-BINDING LIM PROTEIN 1 ISOFORM A; LIM ACTIN-BINDING PROTEIN 1; LIMATIN; ACTIN-BINDING LIM PROTEIN. [RefSeq;Acc:NM_002313] 0.406125729 0.0763094 ABLIM1
81 1.87445 TRANSCRIPTION FACTOR DP-2 (E2F DIMERIZATION PARTNER 2). [SWISSPROT;Acc:Q14188] 0.397822295 0.745698 TFDP2
82 0.505165 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] 0.393307137 0.198685 E2F1
83 0.519607 TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 0.393306865 0.204365 E2F2
84 0.956345 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). [SWISSPROT;Acc:P55010] 0.392699287 0.375556 EIF5
85 2.02915 TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 0.388723357 0.788778 no value
86 3.1266 RGS19-INTERACTING PROTEIN 1 (GAIP C-TERMINUS INTERACTING PROTEIN GIPC) (RGS-GAIP INTERACTING PROTEIN) (TAX INTERACTION PROTEIN 2) (TIP-2). [SWISSPROT;Acc:O14908] 0.385693725 1.20591 GIPC1
87 0.295729 0.38524798 0.113929 PLEKHG6
88 0.30421 APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796] 0.385243746 0.117195 SHROOM2
89 0.396725 0.385224022 0.152828 no value
90 SHROOM-RELATED PROTEIN; F-ACTIN-BINDING PROTEIN; LIKELY ORTHOLOG OF MOUSE SHROOM. [RefSeq;Acc:NM_020859] SHROOM3
91 SHROOM4
92 2.37847 0.38461532 0.914796 no value
93 1.32571 SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [SWISSPROT;Acc:Q13191] 0.378713293 0.502064 CBLB
94 1.04353 CBL E3 UBIQUITIN PROTEIN LIGASE (EC 6.3.2.-) (SIGNAL TRANSDUCTION PROTEIN CBL) (PROTO-ONCOGENE C-CBL). [SWISSPROT;Acc:P22681] 0.378103169 0.394562 CBL
95 0.589242 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 (POTASSIUM CHANNEL KV1.2) (RBK2) (HBK5) (NGK1) (MK2) (HUKIV). [SWISSPROT;Acc:P16389] 0.376042441 0.22158 KCNA2
96 0.494524 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 1 (POTASSIUM CHANNEL KV1.1) (HUKI) (HBK1). [SWISSPROT;Acc:Q09470] 0.375915021 0.185899 KCNA1
97 0.442453 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 4 (POTASSIUM CHANNEL KV1.4) (HK1) (HPCN2) (HBK4) (HUKII). [SWISSPROT;Acc:P22459] 0.375820709 0.166283 KCNA4
98 1.01082 VAV PROTO-ONCOGENE. [SWISSPROT;Acc:P15498] 0.375224076 0.379284 VAV1
99 1.015 VAV-3 PROTEIN. [SWISSPROT;Acc:Q9UKW4] 0.374653202 0.380273 VAV3
100 0.165754 "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]" 0.373794298 0.0619579 INPP4A

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/